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ENH: Add initial FastSurfer interface (WIP) #280

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@pcamach2 pcamach2 commented Apr 26, 2022

Supports #278

Adds FastSurfer detection utility incorporated to smriprep.workflows.anatomical.py to fix failure when providing FastSurfer subjects dir as existing Freesurfer subjects dir. This utility check_fastsurfer employs a fix of touching a labels intensity file expected by Freesurfer, but not currently produced by FastSurfer. FastSurfer outputs from running with the --surfreg flag can then be used to successfully complete the sMRIPrep workflow.

Adds draft of basic interface for FastSurfer to smriprep interfaces, which work on my test datasets when running on the modified Docker or Singularity images (see f8972da for changes to Dockerfile EDIT: this Dockerfile has been replaced with a version built on Ubuntu 20.04 that passes CircleCI build).

To support the using the FastSurfer interface/wrapper to run FastSurfer as part of sMRIPrep, this PR also adds the following argument to the cli (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch-dev/smriprep/cli/run.py)

    g_surfs_xor.add_argument(
        "--fastsurfer-recon",
        action="store_true",
        dest="run_fastsurfer",
        help="enable FastSurfer surface preprocessing.",
    )

As mentioned in the above issue, I am wondering where best to split workflow behavior (in anatomical.py?) based on the above argument. Would it be better to make separate surfaces.py versions for FastSurfer and FreeSurfer or just different workflows within a unified surfaces.py? Note that if a dataset includes FLAIR or T2w, FreeSurfer will still want to process them automatically even if there is FastSurfer output (this adds on a few hours).

Dockerfile building from a PyTorch base image to facilitate running FastSurfer (GPU). Testing this image for FastSurfer - once built as smriprep:fastsurfer_dev - can be performed with the following command:

docker run --gpus all --entrypoint /bin/bash -v /path/to/bids:/data -v /path/to/bids/derivatives/fastsurfer:/output -v /path/to/freesurfer/license:/fs60/license --rm --user `id -u` smriprep:fastsurfer_dev /opt/FastSurfer/run_fastsurfer.sh --fs_license /fs60/license --t1 /data/sourcedata/sub-SUBJECT/ses-SESSION/anat/sub-SUBJECT_ses-SESSION_T1w.nii.gz --sid sub-SUBJECT --sd /output
Checks FreeSurfer subjects dir for presence of files in mri/ with names indicating processing with FastSurfer, and returns a boolean fastsurfer_bool to indicate that FastSurfer is being used instead of Freesurfer. For development purposes, this also touches files that are expected outputs of Freesurfer, but not produced by default in FastSurfer. (Addresses nipreps#278 & Deep-MI/FastSurfer#21)
Add logger for the check_fastsurfer function to indicate if evidence of FastSurfer surface recon was used to generate the given subjects_dir
Adds the check_fastsurfer function call to log FastSurfer outputs detected in subjects_dir and touch mri/aseg.auto_noCCseg.label_intensities.txt to prevent failure in surfaces.py as a temporary fix for nipreps#278
Removes currently unused fastsurfer_bool variable
Adds FastSurfer argument to support FastSurfer as a surface processing option (nipreps#278)
Add citations for FastSurfer: 1mm isotropic original paper = fastsurfer, 2022 hires version (NOT YET IMPLEMENTED) = fastsurfer_hires
Adds python wrapper for FastSurfer (nipreps#278)
Adds affiliation to contributors for work regarding nipreps#278
Fix typo
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pep8speaks commented Apr 26, 2022

Hello @pcamach2! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-09-01 16:21:34 UTC

@pcamach2 pcamach2 marked this pull request as draft April 26, 2022 22:58
pcamach2 added a commit to pcamach2/smriprep that referenced this pull request Apr 27, 2022
Fix fail to build docs in CircleCI observed in testing draft changes made to PR nipreps#280. 

```
#!/bin/bash -eo pipefail
make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html

make: Entering directory '/tmp/gh-pages/docs'
PYTHONPATH=/tmp/gh-pages sphinx-build -b html -d _build/no_version_html/doctrees  -W . _build/no_version_html/html
Traceback (most recent call last):
  File "/home/circleci/.local/bin/sphinx-build", line 5, in <module>
    from sphinx.cmd.build import main
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/cmd/build.py", line 23, in <module>
    from sphinx.application import Sphinx
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/application.py", line 42, in <module>
    from sphinx.highlighting import lexer_classes, lexers
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/highlighting.py", line 30, in <module>
    from sphinx.ext import doctest
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/ext/doctest.py", line 28, in <module>
    from sphinx.builders import Builder
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 24, in <module>
    from sphinx.io import read_doc
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/io.py", line 42, in <module>
    from sphinx.util.rst import append_epilog, docinfo_re, prepend_prolog
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/util/rst.py", line 22, in <module>
    from jinja2 import environmentfilter
ImportError: cannot import name 'environmentfilter' from 'jinja2' (/home/circleci/.local/lib/python3.8/site-packages/jinja2/__init__.py)
make: *** [Makefile:61: html] Error 1
make: Leaving directory '/tmp/gh-pages/docs'

Exited with code exit status 2

CircleCI received exit code 2

```
From suggested fix for similar behavior: mkdocs/mkdocs#2799
Fix fail to build docs in CircleCI observed in testing draft changes made to PR nipreps#280. 

```
#!/bin/bash -eo pipefail
make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html

make: Entering directory '/tmp/gh-pages/docs'
PYTHONPATH=/tmp/gh-pages sphinx-build -b html -d _build/no_version_html/doctrees  -W . _build/no_version_html/html
Traceback (most recent call last):
  File "/home/circleci/.local/bin/sphinx-build", line 5, in <module>
    from sphinx.cmd.build import main
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/cmd/build.py", line 23, in <module>
    from sphinx.application import Sphinx
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/application.py", line 42, in <module>
    from sphinx.highlighting import lexer_classes, lexers
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/highlighting.py", line 30, in <module>
    from sphinx.ext import doctest
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/ext/doctest.py", line 28, in <module>
    from sphinx.builders import Builder
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 24, in <module>
    from sphinx.io import read_doc
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/io.py", line 42, in <module>
    from sphinx.util.rst import append_epilog, docinfo_re, prepend_prolog
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/util/rst.py", line 22, in <module>
    from jinja2 import environmentfilter
ImportError: cannot import name 'environmentfilter' from 'jinja2' (/home/circleci/.local/lib/python3.8/site-packages/jinja2/__init__.py)
make: *** [Makefile:61: html] Error 1
make: Leaving directory '/tmp/gh-pages/docs'

Exited with code exit status 2

CircleCI received exit code 2

```
From suggested fix for similar behavior: mkdocs/mkdocs#2799
@effigies
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Ah, I'm really sorry about the slow response times. I think I saw this in the middle of something else and then the notification got buried. Do you want help resolving merge conflicts?

@pcamach2
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No worries! Any help with the merge conflicts would be great, thanks!

@effigies
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effigies commented Mar 22, 2024

@pcamach2 Sorry I haven't been able to give this the attention it deserves. I want to check in with whether the --fs-no-resume option introduced in #393 will solve your problems, in the sense of allowing FastSurfer outputs to be used?

@pcamach2
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@effigies, no worries! A lot has been updated for both toolkits in the meantime, so I processed a dataset with the latest FastSurfer (v2.2.0) and then used it as an input for sMRIPrep v0.15.0 with the --fs-no-resume argument as you suggested. However, it fails during the midthickness workflow:

$ SINGULARITYENV_MPLCONFIGDIR=/work_dir singularity run --cleanenv -B BICpipeline/beta/testing/PROJECT/bids:/data,./scratch:/work_dir,/home/pcamach2/dev/singularity/license.txt:/opt/freesurfer/license.txt smriprep-v0.15.0.sif /data/sourcedata /data/derivatives/smriprep --fs-license-file /opt/freesurfer/license.txt --fs-subjects-dir /data/derivatives/fastsurfer --fs-no-resume  participant --participant_label PROJECT107
240322-22:30:49,789 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.15.0:
      * BIDS dataset path: /data/sourcedata.
      * Participant list: ['PROJECT107'].
      * Run identifier: 20240322-223049_9f89222c-f85f-4898-b250-c2a53be624e6.

    Spatial References: <none>.
    
240322-22:30:55,71 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
240322-22:30:55,323 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
240322-22:30:57,72 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
240322-22:30:57,75 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
240322-22:30:57,89 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
240322-22:30:57,91 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
240322-22:30:57,91 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240322-22:30:57,102 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240322-22:30:57,107 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
240322-22:30:57,110 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
240322-22:30:57,113 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
240322-22:31:00,190 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.15.0
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.8.6
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset. The T1w image was corrected for intensity
non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.5.1
[@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL (version unknown), RRID:SCR_002823, @fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 7.3.2,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


240322-22:31:05,747 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
240322-22:31:05,748 nipype.workflow INFO:
	 [Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
240322-22:31:05,874 nipype.workflow INFO:
	 [Node] Finished "res_tmpl", elapsed time 0.117542s.
240322-22:31:05,874 nipype.workflow WARNING:
	 Storing result file without outputs
240322-22:31:05,875 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" (/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl)
240322-22:31:07,379 nipype.workflow ERROR:
	 Node res_tmpl failed to run on host BI-paul-thinkpad.
240322-22:31:07,380 nipype.workflow ERROR:
	 Saving crash info to /data/derivatives/smriprep/smriprep/sub-PROJECT107/log/20240322-223049_9f89222c-f85f-4898-b250-c2a53be624e6/crash-20240322-223107-smriprep-res_tmpl-467f74f4-82bf-4ee6-9558-573728fc6a98.txt
Traceback (most recent call last):
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node res_tmpl.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/niworkflows/interfaces/nibabel.py", line 314, in _run_interface
	    resample_by_spacing(
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/niworkflows/utils/images.py", line 255, in resample_by_spacing
	    data = gaussian_filter(in_file.get_fdata(), smooth)
	                           ^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
	    data = np.asanyarray(self._dataobj, dtype=dtype)
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
	    arr = self._get_scaled(dtype=dtype, slicer=())
	          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
	    scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
	                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
	    return array_from_file(
	           ^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
	    raise OSError(
	OSError: Expected 64364544 bytes, got 19915580 bytes from object
	 - could the file be damaged?


240322-22:31:07,459 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fs_isrunning".
240322-22:31:07,459 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning".
240322-22:31:07,461 nipype.workflow INFO:
	 [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
240322-22:31:07,462 nipype.workflow INFO:
	 [Node] Finished "fs_isrunning", elapsed time 0.000529s.
240322-22:31:09,512 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fs_base_inputs" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fs_base_inputs".
240322-22:31:09,514 nipype.workflow INFO:
	 [Node] Executing "fs_base_inputs" <nipype.interfaces.io.FreeSurferSource>
240322-22:31:09,519 nipype.workflow INFO:
	 [Node] Finished "fs_base_inputs", elapsed time 0.005211s.
240322-22:31:09,521 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/get_surfaces".
240322-22:31:09,522 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:31:09,525 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.003238s.
240322-22:31:16,162 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240322-22:31:16,163 nipype.workflow INFO:
	 [Node] Executing "_midthickness1" <smriprep.interfaces.freesurfer.MakeMidthickness>
240322-22:31:16,163 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240322-22:31:16,165 nipype.workflow INFO:
	 [Node] Executing "_midthickness0" <smriprep.interfaces.freesurfer.MakeMidthickness>
240322-22:31:17,933 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm".
240322-22:31:17,933 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm".
240322-22:31:17,934 nipype.workflow INFO:
	 [Node] Executing "fsnative2t1w_xfm" <niworkflows.interfaces.freesurfer.PatchedRobustRegister>
240322-22:32:25,109 nipype.workflow INFO:
	 [Node] Finished "fsnative2t1w_xfm", elapsed time 67.172965s.
Captured warning (<class 'UserWarning'>): Reference space not set
240322-22:38:48,134 nipype.workflow INFO:
	 [Node] Finished "_midthickness1", elapsed time 451.969496s.
240322-22:38:48,688 nipype.workflow INFO:
	 [Node] Finished "_midthickness0", elapsed time 452.522994s.
240322-22:38:50,233 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] "_midthickness0" found cached.
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240322-22:38:50,235 nipype.workflow INFO:
	 [Node] Cached "_midthickness1" - collecting precomputed outputs
240322-22:38:50,235 nipype.workflow INFO:
	 [Node] "_midthickness1" found cached.
240322-22:38:51,479 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/save_midthickness".
240322-22:38:51,483 nipype.workflow INFO:
	 [Node] Executing "save_midthickness" <nipype.interfaces.io.DataSink>
240322-22:38:51,508 nipype.workflow INFO:
	 [Node] Finished "save_midthickness", elapsed time 0.024986s.
240322-22:38:53,479 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.sync" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/sync".
240322-22:38:53,481 nipype.workflow INFO:
	 [Node] Executing "sync" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:53,482 nipype.workflow INFO:
	 [Node] Finished "sync", elapsed time 0.000458s.
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_surface_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/get_surfaces".
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/get_surfaces".
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_spheres_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/get_surfaces".
240322-22:38:55,491 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,492 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,492 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,494 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.002157s.
240322-22:38:55,495 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.00197s.
240322-22:38:55,496 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/fs_datasource".
240322-22:38:55,497 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.recon_report" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/recon_report".
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.006057s.
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Executing "recon_report" <smriprep.interfaces.reports.FSSurfaceReport>
240322-22:38:55,500 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_surface_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/get_surfaces".
240322-22:38:55,501 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,502 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.000615s.
240322-22:38:55,502 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.004462s.
240322-22:38:55,503 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/get_surfaces".
240322-22:38:55,504 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/fs_datasource".
240322-22:38:55,504 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,505 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,507 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.003351s.
240322-22:38:55,509 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/fs_datasource".
240322-22:38:55,510 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,511 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.005807s.
240322-22:38:55,513 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003306s.
240322-22:39:01,485 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:01,485 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:01,486 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,486 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,616 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:01,617 nipype.workflow INFO:
	 [Node] Executing "_fs2gii2" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,620 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
240322-22:39:01,621 nipype.workflow INFO:
	 [Node] Executing "_fs2gii4" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,624 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:01,625 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
240322-22:39:01,626 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,626 nipype.workflow INFO:
	 [Node] Executing "_fs2gii5" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,646 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:01,648 nipype.workflow INFO:
	 [Node] Executing "_fs2gii3" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,111 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:02,112 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,123 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:02,124 nipype.workflow INFO:
	 [Node] Executing "_fs2gii2" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,130 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:02,132 nipype.workflow INFO:
	 [Node] Executing "_fs2gii3" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,204 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:02,206 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,231 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:02,233 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,538 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 1.051215s.
240322-22:39:02,634 nipype.workflow INFO:
	 [Node] Finished "_fs2gii3", elapsed time 0.983534s.
240322-22:39:02,644 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 1.016431s.
240322-22:39:02,650 nipype.workflow INFO:
	 [Node] Finished "_fs2gii5", elapsed time 1.021706s.
240322-22:39:02,667 nipype.workflow INFO:
	 [Node] Finished "_fs2gii4", elapsed time 1.043802s.
240322-22:39:03,5 nipype.workflow INFO:
	 [Node] Finished "_fs2gii2", elapsed time 1.3857300000000001s.
240322-22:39:03,57 nipype.workflow INFO:
	 [Node] Finished "_fs2gii3", elapsed time 0.922497s.
240322-22:39:03,88 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 1.60118s.
240322-22:39:03,108 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 0.900182s.
240322-22:39:03,136 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 0.901023s.
240322-22:39:03,265 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 1.150844s.
240322-22:39:03,441 nipype.workflow INFO:
	 [Node] Finished "_fs2gii2", elapsed time 1.315556s.
240322-22:39:03,544 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:03,548 nipype.workflow INFO:
	 [Node] Cached "_fs2gii2" - collecting precomputed outputs
240322-22:39:03,548 nipype.workflow INFO:
	 [Node] "_fs2gii2" found cached.
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] Cached "_fs2gii3" - collecting precomputed outputs
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] "_fs2gii3" found cached.
240322-22:39:03,550 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] Cached "_fs2gii4" - collecting precomputed outputs
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] "_fs2gii4" found cached.
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
240322-22:39:03,552 nipype.workflow INFO:
	 [Node] Cached "_fs2gii5" - collecting precomputed outputs
240322-22:39:03,552 nipype.workflow INFO:
	 [Node] "_fs2gii5" found cached.
240322-22:39:05,245 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii2".
240322-22:39:05,246 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii2" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,272 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:05,273 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii0" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,319 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:05,320 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii1" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,506 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] Cached "_fs2gii2" - collecting precomputed outputs
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] "_fs2gii2" found cached.
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:05,510 nipype.workflow INFO:
	 [Node] Cached "_fs2gii3" - collecting precomputed outputs
240322-22:39:05,510 nipype.workflow INFO:
	 [Node] "_fs2gii3" found cached.
240322-22:39:05,533 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii3".
240322-22:39:05,534 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii3" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,535 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:05,536 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii1" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,541 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:05,542 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii0" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,856 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii2", elapsed time 0.608711s.
240322-22:39:05,916 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii0", elapsed time 0.641329s.
240322-22:39:05,916 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii1", elapsed time 0.594376s.
240322-22:39:06,72 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii3", elapsed time 0.536187s.
240322-22:39:06,72 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii1", elapsed time 0.534703s.
240322-22:39:06,87 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii0", elapsed time 0.543845s.
240322-22:39:07,565 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:07,566 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs2" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:08,57 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs2", elapsed time 0.490073s.
240322-22:39:09,569 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:09,578 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,619 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:09,619 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:09,621 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs2" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,621 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs3" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,961 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs2", elapsed time 0.339545s.
240322-22:39:10,68 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
240322-22:39:10,68 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs5" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,107 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:10,108 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,140 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:10,140 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,147 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:10,148 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,171 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.591632s.
240322-22:39:10,200 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs3", elapsed time 0.578916s.
240322-22:39:10,374 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs5", elapsed time 0.305434s.
240322-22:39:10,443 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.302553s.
240322-22:39:10,462 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.352803s.
240322-22:39:10,464 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii0" - collecting precomputed outputs
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] "_morphs2gii0" found cached.
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii1" - collecting precomputed outputs
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] "_morphs2gii1" found cached.
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii2".
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii2" - collecting precomputed outputs
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] "_morphs2gii2" found cached.
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii3".
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii3" - collecting precomputed outputs
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] "_morphs2gii3" found cached.
240322-22:39:10,494 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.34468s.
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii0" - collecting precomputed outputs
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] "_morphs2gii0" found cached.
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii1" - collecting precomputed outputs
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] "_morphs2gii1" found cached.
240322-22:39:11,431 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:11,432 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs3" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,437 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
240322-22:39:11,438 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs4" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,440 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:11,441 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,736 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs3", elapsed time 0.303252s.
240322-22:39:11,741 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs4", elapsed time 0.302262s.
240322-22:39:11,749 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.307808s.
240322-22:39:12,388 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:12,389 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:12,690 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.300547s.
240322-22:39:13,535 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs2" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs2" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs3" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs3" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs2" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs2" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs3" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs3" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs4" - collecting precomputed outputs
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] "_fix_surfs4" found cached.
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
240322-22:39:13,540 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs5" - collecting precomputed outputs
240322-22:39:13,540 nipype.workflow INFO:
	 [Node] "_fix_surfs5" found cached.
240322-22:39:14,490 nipype.workflow INFO:
	 [Node] Finished "recon_report", elapsed time 18.991506s.
240322-22:39:15,978 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1".
240322-22:39:15,978 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0".
240322-22:39:15,979 nipype.workflow INFO:
	 [Node] Executing "_invert_sulc1" <smriprep.interfaces.gifti.MetricMath>
240322-22:39:15,979 nipype.workflow INFO:
	 [Node] Executing "_invert_sulc0" <smriprep.interfaces.gifti.MetricMath>
240322-22:39:15,997 nipype.workflow INFO:
	 [Node] Finished "_invert_sulc1", elapsed time 0.017401s.
240322-22:39:16,0 nipype.workflow INFO:
	 [Node] Finished "_invert_sulc0", elapsed time 0.020199s.
240322-22:39:17,641 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0".
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Cached "_invert_sulc0" - collecting precomputed outputs
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] "_invert_sulc0" found cached.
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1".
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Cached "_invert_sulc1" - collecting precomputed outputs
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] "_invert_sulc1" found cached.
240322-22:39:20,414 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject1".
240322-22:39:20,415 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject0".
240322-22:39:20,416 nipype.workflow INFO:
	 [Node] Executing "_project_unproject1" <smriprep.interfaces.workbench.SurfaceSphereProjectUnproject>
240322-22:39:20,416 nipype.workflow INFO:
	 [Node] Executing "_project_unproject0" <smriprep.interfaces.workbench.SurfaceSphereProjectUnproject>
240322-22:39:22,490 nipype.workflow INFO:
	 [Node] Finished "_project_unproject0", elapsed time 1.78163s.
240322-22:39:22,518 nipype.workflow INFO:
	 [Node] Finished "_project_unproject1", elapsed time 1.768811s.
240322-22:39:23,489 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject0".
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] Cached "_project_unproject0" - collecting precomputed outputs
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] "_project_unproject0" found cached.
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject1".
240322-22:39:23,491 nipype.workflow INFO:
	 [Node] Cached "_project_unproject1" - collecting precomputed outputs
240322-22:39:23,491 nipype.workflow INFO:
	 [Node] "_project_unproject1" found cached.
240322-22:39:33,485 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240322-22:39:33,485 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240322-22:39:33,486 nipype.workflow INFO:
	 [Node] Executing "_regress_affine1" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240322-22:39:33,486 nipype.workflow INFO:
	 [Node] Executing "_regress_affine0" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240322-22:39:33,828 nipype.workflow INFO:
	 [Node] Finished "_regress_affine0", elapsed time 0.20802s.
240322-22:39:33,833 nipype.workflow INFO:
	 [Node] Finished "_regress_affine1", elapsed time 0.212368s.
240322-22:39:35,499 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] Cached "_regress_affine0" - collecting precomputed outputs
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] "_regress_affine0" found cached.
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240322-22:39:35,501 nipype.workflow INFO:
	 [Node] Cached "_regress_affine1" - collecting precomputed outputs
240322-22:39:35,501 nipype.workflow INFO:
	 [Node] "_regress_affine1" found cached.
240322-22:39:39,498 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240322-22:39:39,499 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240322-22:39:39,500 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine0" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240322-22:39:39,500 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine1" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240322-22:39:40,53 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine0", elapsed time 0.428945s.
240322-22:39:40,83 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine1", elapsed time 0.444635s.
240322-22:39:41,510 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240322-22:39:41,511 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine0" - collecting precomputed outputs
240322-22:39:41,511 nipype.workflow INFO:
	 [Node] "_apply_surface_affine0" found cached.
240322-22:39:41,512 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240322-22:39:41,513 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine1" - collecting precomputed outputs
240322-22:39:41,513 nipype.workflow INFO:
	 [Node] "_apply_surface_affine1" found cached.
240322-22:39:45,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240322-22:39:45,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240322-22:39:45,502 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere0" <smriprep.interfaces.workbench.SurfaceModifySphere>
240322-22:39:45,502 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere1" <smriprep.interfaces.workbench.SurfaceModifySphere>
240322-22:39:46,87 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere0", elapsed time 0.443699s.
240322-22:39:46,89 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere1", elapsed time 0.444591s.
240322-22:39:47,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere0" - collecting precomputed outputs
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] "_modify_sphere0" found cached.
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240322-22:39:47,503 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere1" - collecting precomputed outputs
240322-22:39:47,503 nipype.workflow INFO:
	 [Node] "_modify_sphere1" found cached.
240322-22:39:51,500 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240322-22:39:51,500 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240322-22:39:51,502 nipype.workflow INFO:
	 [Node] Executing "_msmsulc0" <smriprep.interfaces.msm.MSM>
240322-22:39:51,502 nipype.workflow INFO:
	 [Node] Executing "_msmsulc1" <smriprep.interfaces.msm.MSM>
240322-23:02:37,720 nipype.workflow INFO:
	 [Node] Finished "_msmsulc1", elapsed time 1366.217513s.
240322-23:02:41,830 nipype.workflow INFO:
	 [Node] Finished "_msmsulc0", elapsed time 1370.327796s.
240322-23:02:43,641 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] Cached "_msmsulc0" - collecting precomputed outputs
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] "_msmsulc0" found cached.
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240322-23:02:43,649 nipype.workflow INFO:
	 [Node] Cached "_msmsulc1" - collecting precomputed outputs
240322-23:02:43,649 nipype.workflow INFO:
	 [Node] "_msmsulc1" found cached.
240322-23:02:51,556 nipype.workflow ERROR:
	 could not run node: smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl
Preprocessing did not finish successfully. Errors occurred while processing data from participants: PROJECT107 (1). Check the HTML reports for details.

@effigies
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Looks like midthickness worked, but templateflow failed to download the whole file either during image creation or at runtime.

@pcamach2
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Ah, my mistake. The midthickness issue popped up when I used output from an older version of FastSurfer (version < 2.X).

I pulled a local copy of the templates with datalad and the workflow completes now.

$ SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow SINGULARITYENV_MPLCONFIGDIR=/work_dir singularity run --cleanenv -B BICpipeline/beta/testing/PROJECT/bids:/data,./templateflow:/templateflow,/home/pcamach2/dev/singularity/license.txt:/opt/freesurfer/license.txt smriprep-v0.15.0.sif /data/sourcedata /data/derivatives/smriprep --fs-license-file /opt/freesurfer/license.txt --fs-subjects-dir /data/derivatives/fastsurfer --fs-no-resume  participant --participant_label PROJECT107
240323-15:32:46,26 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.15.0:
      * BIDS dataset path: /data/sourcedata.
      * Participant list: ['PROJECT107'].
      * Run identifier: 20240323-153245_05a2bfa8-c5dc-44c6-bee0-cab90fa6b1ad.

    Spatial References: <none>.
    
240323-15:32:51,507 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
240323-15:32:51,817 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 32.4M/32.4M [00:01<00:00, 18.6MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 2.59M/2.59M [00:00<00:00, 7.40MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 265k/265k [00:00<00:00, 2.18MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_probseg.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 4.06M/4.06M [00:00<00:00, 13.7MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_probseg.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 447k/447k [00:00<00:00, 3.50MB/s]
240323-15:32:57,810 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
240323-15:32:57,814 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
240323-15:32:57,827 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
240323-15:32:57,829 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
240323-15:32:57,829 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240323-15:32:57,841 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240323-15:32:57,845 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
240323-15:32:57,848 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
240323-15:32:57,850 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
240323-15:33:00,875 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.15.0
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.8.6
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset. The T1w image was corrected for intensity
non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.5.1
[@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL (version unknown), RRID:SCR_002823, @fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 7.3.2,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


240323-15:33:04,40 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.full_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/full_wm".
240323-15:33:04,40 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.full_wm".
240323-15:33:04,49 nipype.workflow INFO:
	 [Node] Executing "full_wm" <nipype.interfaces.utility.wrappers.Function>
240323-15:33:04,75 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.lap_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/lap_tmpl".
240323-15:33:04,75 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.lap_tmpl".
240323-15:33:04,76 nipype.workflow INFO:
	 [Node] Executing "lap_tmpl" <nipype.interfaces.ants.utils.ImageMath>
240323-15:33:04,123 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
240323-15:33:04,124 nipype.workflow INFO:
	 [Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
240323-15:33:04,374 nipype.workflow INFO:
	 [Node] Finished "full_wm", elapsed time 0.322995s.
240323-15:33:04,979 nipype.workflow INFO:
	 [Node] Finished "res_tmpl", elapsed time 0.853718s.
240323-15:33:07,666 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fs_isrunning".
240323-15:33:07,668 nipype.workflow INFO:
	 [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
240323-15:33:07,669 nipype.workflow INFO:
	 [Node] Finished "fs_isrunning", elapsed time 0.000589s.
240323-15:33:09,731 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fs_base_inputs" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fs_base_inputs".
240323-15:33:09,733 nipype.workflow INFO:
	 [Node] Executing "fs_base_inputs" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:09,733 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/get_surfaces".
240323-15:33:09,734 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:09,739 nipype.workflow INFO:
	 [Node] Finished "fs_base_inputs", elapsed time 0.005764s.
240323-15:33:09,739 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.005142s.
240323-15:33:10,281 nipype.workflow INFO:
	 [Node] Finished "lap_tmpl", elapsed time 6.109642s.
240323-15:33:11,679 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.mrg_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/mrg_tmpl".
240323-15:33:11,679 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.mrg_tmpl".
240323-15:33:11,680 nipype.workflow INFO:
	 [Node] Executing "mrg_tmpl" <nipype.interfaces.utility.base.Merge>
240323-15:33:11,681 nipype.workflow INFO:
	 [Node] Finished "mrg_tmpl", elapsed time 0.000157s.
240323-15:33:16,410 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240323-15:33:16,410 nipype.workflow INFO:
	 [Node] Outdated cache found for "_midthickness1".
240323-15:33:16,421 nipype.workflow INFO:
	 [Node] Executing "_midthickness1" <smriprep.interfaces.freesurfer.MakeMidthickness>
240323-15:33:16,421 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240323-15:33:16,422 nipype.workflow INFO:
	 [Node] Outdated cache found for "_midthickness0".
240323-15:33:16,423 nipype.workflow INFO:
	 [Node] Executing "_midthickness0" <smriprep.interfaces.freesurfer.MakeMidthickness>
240323-15:33:16,549 nipype.workflow INFO:
	 [Node] Finished "_midthickness0", elapsed time 0.124941s.
240323-15:33:16,556 nipype.workflow INFO:
	 [Node] Finished "_midthickness1", elapsed time 0.135097s.
240323-15:33:20,393 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.midthickness".
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] "_midthickness0" found cached.
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] Cached "_midthickness1" - collecting precomputed outputs
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] "_midthickness1" found cached.
240323-15:33:21,677 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/save_midthickness".
240323-15:33:21,677 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness".
240323-15:33:21,678 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.init_aff" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/init_aff".
240323-15:33:21,680 nipype.workflow INFO:
	 [Node] Executing "save_midthickness" <nipype.interfaces.io.DataSink>
240323-15:33:21,684 nipype.workflow INFO:
	 [Node] Executing "init_aff" <nipype.interfaces.ants.utils.AI>
240323-15:33:21,721 nipype.workflow INFO:
	 [Node] Finished "save_midthickness", elapsed time 0.04123s.
240323-15:33:25,674 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/get_surfaces".
240323-15:33:25,675 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/fs_datasource".
240323-15:33:25,675 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,677 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,683 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.006181s.
240323-15:33:25,683 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.007481s.
240323-15:33:25,686 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/get_surfaces".
240323-15:33:25,686 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.recon_report" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/recon_report".
240323-15:33:25,687 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,687 nipype.workflow INFO:
	 [Node] Executing "recon_report" <smriprep.interfaces.reports.FSSurfaceReport>
240323-15:33:25,789 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.101639s.
240323-15:33:25,791 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/fs_datasource".
240323-15:33:25,792 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,796 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003723s.
240323-15:33:25,798 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/fs_datasource".
240323-15:33:25,798 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,803 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003996s.
240323-15:33:32,149 nipype.workflow INFO:
	 [Node] Finished "init_aff", elapsed time 10.464129s.
240323-15:33:33,670 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.norm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/norm".
240323-15:33:33,686 nipype.workflow INFO:
	 [Node] Executing "norm" <niworkflows.interfaces.fixes.FixHeaderRegistration>
240323-15:33:42,230 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240323-15:33:42,230 nipype.workflow INFO:
	 [Node] Outdated cache found for "_fix_surfs0".
240323-15:33:42,241 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240323-15:33:42,316 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240323-15:33:42,317 nipype.workflow INFO:
	 [Node] Outdated cache found for "_fix_surfs1".
240323-15:33:42,318 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240323-15:33:42,559 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.316107s.
240323-15:33:42,627 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.307268s.
240323-15:33:43,461 nipype.workflow INFO:
	 [Node] Finished "recon_report", elapsed time 17.773253s.
240323-15:33:46,266 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_surface_wf.fix_surfs".
240323-15:33:46,267 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240323-15:33:59,685 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240323-15:33:59,686 nipype.workflow INFO:
	 [Node] Outdated cache found for "_regress_affine1".
240323-15:33:59,687 nipype.workflow INFO:
	 [Node] Executing "_regress_affine1" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240323-15:34:00,233 nipype.workflow INFO:
	 [Node] Finished "_regress_affine1", elapsed time 0.172088s.
240323-15:34:02,154 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240323-15:34:02,154 nipype.workflow INFO:
	 [Node] Outdated cache found for "_regress_affine0".
240323-15:34:02,156 nipype.workflow INFO:
	 [Node] Executing "_regress_affine0" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240323-15:34:02,562 nipype.workflow INFO:
	 [Node] Finished "_regress_affine0", elapsed time 0.238096s.
240323-15:34:03,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.regress_affine".
240323-15:34:03,673 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] Cached "_regress_affine0" - collecting precomputed outputs
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] "_regress_affine0" found cached.
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240323-15:34:03,675 nipype.workflow INFO:
	 [Node] Cached "_regress_affine1" - collecting precomputed outputs
240323-15:34:03,675 nipype.workflow INFO:
	 [Node] "_regress_affine1" found cached.
240323-15:34:07,674 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240323-15:34:07,674 nipype.workflow INFO:
	 [Node] Outdated cache found for "_apply_surface_affine0".
240323-15:34:07,675 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine0" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240323-15:34:07,676 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240323-15:34:07,676 nipype.workflow INFO:
	 [Node] Outdated cache found for "_apply_surface_affine1".
240323-15:34:07,677 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine1" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240323-15:34:08,232 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine1", elapsed time 0.459004s.
240323-15:34:08,306 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine0", elapsed time 0.494098s.
240323-15:34:09,679 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.apply_surface_affine".
240323-15:34:09,681 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine0" - collecting precomputed outputs
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] "_apply_surface_affine0" found cached.
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine1" - collecting precomputed outputs
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] "_apply_surface_affine1" found cached.
240323-15:34:13,670 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "_modify_sphere0".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "_modify_sphere1".
240323-15:34:13,672 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere0" <smriprep.interfaces.workbench.SurfaceModifySphere>
240323-15:34:13,672 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere1" <smriprep.interfaces.workbench.SurfaceModifySphere>
240323-15:34:14,172 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere1", elapsed time 0.417555s.
240323-15:34:14,177 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere0", elapsed time 0.408467s.
240323-15:34:15,704 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.modify_sphere".
240323-15:34:15,706 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere0" - collecting precomputed outputs
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] "_modify_sphere0" found cached.
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240323-15:34:15,708 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere1" - collecting precomputed outputs
240323-15:34:15,708 nipype.workflow INFO:
	 [Node] "_modify_sphere1" found cached.
240323-15:34:19,711 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Outdated cache found for "_msmsulc0".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Outdated cache found for "_msmsulc1".
240323-15:34:19,713 nipype.workflow INFO:
	 [Node] Executing "_msmsulc0" <smriprep.interfaces.msm.MSM>
240323-15:34:19,714 nipype.workflow INFO:
	 [Node] Executing "_msmsulc1" <smriprep.interfaces.msm.MSM>
240323-15:38:50,980 nipype.workflow INFO:
	 [Node] Finished "norm", elapsed time 317.190996s.
240323-15:38:51,699 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.map_wmmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/map_wmmask".
240323-15:38:51,700 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.map_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/map_brainmask".
240323-15:38:51,704 nipype.workflow INFO:
	 [Node] Executing "map_wmmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
240323-15:38:51,705 nipype.workflow INFO:
	 [Node] Executing "map_brainmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
240323-15:39:08,543 nipype.workflow INFO:
	 [Node] Finished "map_brainmask", elapsed time 16.687305s.
240323-15:39:08,815 nipype.workflow INFO:
	 [Node] Finished "map_wmmask", elapsed time 17.019473s.
240323-15:39:09,690 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.thr_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/thr_brainmask".
240323-15:39:09,691 nipype.workflow INFO:
	 [Node] Executing "thr_brainmask" <nipype.interfaces.ants.utils.ThresholdImage>
240323-15:39:09,707 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
240323-15:39:09,708 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
240323-15:39:10,607 nipype.workflow INFO:
	 [Node] Finished "thr_brainmask", elapsed time 0.915399s.
240323-15:39:11,692 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
240323-15:39:11,692 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
240323-15:39:11,694 nipype.workflow INFO:
	 [Node] Executing "dil_brainmask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:11,694 nipype.workflow INFO:
	 [Node] Executing "03_pad_mask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:12,327 nipype.workflow INFO:
	 [Node] Finished "03_pad_mask", elapsed time 0.632806s.
240323-15:39:12,803 nipype.workflow INFO:
	 [Node] Finished "dil_brainmask", elapsed time 1.108915s.
240323-15:39:13,696 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/get_brainmask".
240323-15:39:13,698 nipype.workflow INFO:
	 [Node] Executing "get_brainmask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:14,789 nipype.workflow INFO:
	 [Node] Finished "get_brainmask", elapsed time 1.090463s.
240323-15:39:31,153 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 21.309572s.
240323-15:39:31,689 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/01_atropos".
240323-15:39:31,690 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
240323-15:39:31,691 nipype.workflow INFO:
	 [Node] Executing "01_atropos" <nipype.interfaces.ants.segmentation.Atropos>
240323-15:39:31,691 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:39:32,662 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 0.970423s.
240323-15:40:07,97 nipype.workflow INFO:
	 [Node] Finished "01_atropos", elapsed time 35.405753s.
240323-15:40:07,706 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
240323-15:40:07,707 nipype.workflow INFO:
	 [Node] Executing "02_pad_segm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:08,486 nipype.workflow INFO:
	 [Node] Finished "02_pad_segm", elapsed time 0.778429s.
240323-15:40:09,693 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
240323-15:40:09,694 nipype.workflow INFO:
	 [Node] Executing "04_sel_labels" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:09,968 nipype.workflow INFO:
	 [Node] Finished "04_sel_labels", elapsed time 0.27416s.
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/06_get_gm".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/05_get_wm".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/10_me_csf".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "06_get_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "10_me_csf" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "27_depad_csf" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,606 nipype.workflow INFO:
	 [Node] Executing "05_get_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:13,193 nipype.workflow INFO:
	 [Node] Finished "27_depad_csf", elapsed time 0.587024s.
240323-15:40:13,888 nipype.workflow INFO:
	 [Node] Finished "05_get_wm", elapsed time 1.281898s.
240323-15:40:13,936 nipype.workflow INFO:
	 [Node] Finished "06_get_gm", elapsed time 1.330852s.
240323-15:40:14,610 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
240323-15:40:14,610 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
240323-15:40:14,611 nipype.workflow INFO:
	 [Node] Executing "07_fill_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:14,612 nipype.workflow INFO:
	 [Node] Executing "09_relabel_wm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:15,254 nipype.workflow INFO:
	 [Node] Finished "09_relabel_wm", elapsed time 0.64159s.
240323-15:40:15,840 nipype.workflow INFO:
	 [Node] Finished "10_me_csf", elapsed time 3.234402s.
240323-15:40:16,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
240323-15:40:16,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
240323-15:40:16,609 nipype.workflow INFO:
	 [Node] Executing "26_depad_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:16,614 nipype.workflow INFO:
	 [Node] Executing "apply_wm_prior" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:17,289 nipype.workflow INFO:
	 [Node] Finished "26_depad_wm", elapsed time 0.678833s.
240323-15:40:17,398 nipype.workflow INFO:
	 [Node] Finished "apply_wm_prior", elapsed time 0.783783s.
240323-15:40:18,610 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
240323-15:40:18,611 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
240323-15:40:24,620 nipype.workflow INFO:
	 [Node] Finished "07_fill_gm", elapsed time 10.008911s.
240323-15:40:26,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
240323-15:40:26,612 nipype.workflow INFO:
	 [Node] Executing "08_mult_gm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:27,441 nipype.workflow INFO:
	 [Node] Finished "08_mult_gm", elapsed time 0.829026s.
240323-15:40:28,623 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/11_add_gm".
240323-15:40:28,625 nipype.workflow INFO:
	 [Node] Executing "11_add_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:30,37 nipype.workflow INFO:
	 [Node] Finished "11_add_gm", elapsed time 1.412401s.
240323-15:40:30,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
240323-15:40:30,610 nipype.workflow INFO:
	 [Node] Executing "12_relabel_gm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:31,271 nipype.workflow INFO:
	 [Node] Finished "12_relabel_gm", elapsed time 0.65975s.
240323-15:40:32,620 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
240323-15:40:32,620 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
240323-15:40:32,621 nipype.workflow INFO:
	 [Node] Executing "25_depad_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:32,621 nipype.workflow INFO:
	 [Node] Executing "13_add_gm_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:33,359 nipype.workflow INFO:
	 [Node] Finished "25_depad_gm", elapsed time 0.737597s.
240323-15:40:34,244 nipype.workflow INFO:
	 [Node] Finished "13_add_gm_wm", elapsed time 1.622328s.
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/merge_tpms".
240323-15:40:34,612 nipype.workflow INFO:
	 [Node] Executing "24_depad_segm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:34,612 nipype.workflow INFO:
	 [Node] Executing "14_sel_labels2" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:34,614 nipype.workflow INFO:
	 [Node] Executing "merge_tpms" <nipype.interfaces.utility.base.Merge>
240323-15:40:34,614 nipype.workflow INFO:
	 [Node] Finished "merge_tpms", elapsed time 0.000187s.
240323-15:40:34,806 nipype.workflow INFO:
	 [Node] Finished "14_sel_labels2", elapsed time 0.1936s.
240323-15:40:35,329 nipype.workflow INFO:
	 [Node] Finished "24_depad_segm", elapsed time 0.716292s.
240323-15:40:36,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/15_add_7".
240323-15:40:36,610 nipype.workflow INFO:
	 [Node] Executing "15_add_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:37,775 nipype.workflow INFO:
	 [Node] Finished "15_add_7", elapsed time 1.164979s.
240323-15:40:38,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/16_me_7".
240323-15:40:38,613 nipype.workflow INFO:
	 [Node] Executing "16_me_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:40,444 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 21.832634s.
240323-15:40:41,188 nipype.workflow INFO:
	 [Node] Finished "16_me_7", elapsed time 2.5746700000000002s.
240323-15:40:42,609 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/17_comp_7".
240323-15:40:42,610 nipype.workflow INFO:
	 [Node] Executing "17_comp_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:43,936 nipype.workflow INFO:
	 [Node] Finished "17_comp_7", elapsed time 1.325434s.
240323-15:40:44,607 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/18_md_7".
240323-15:40:44,608 nipype.workflow INFO:
	 [Node] Executing "18_md_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:45,942 nipype.workflow INFO:
	 [Node] Finished "18_md_7", elapsed time 1.33344s.
240323-15:40:46,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/19_fill_7".
240323-15:40:46,612 nipype.workflow INFO:
	 [Node] Executing "19_fill_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:56,88 nipype.workflow INFO:
	 [Node] Finished "19_fill_7", elapsed time 9.475285s.
240323-15:40:56,613 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
240323-15:40:56,615 nipype.workflow INFO:
	 [Node] Executing "20_add_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:57,938 nipype.workflow INFO:
	 [Node] Finished "20_add_7_2", elapsed time 1.322305s.
240323-15:40:58,612 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
240323-15:40:58,613 nipype.workflow INFO:
	 [Node] Executing "21_md_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:59,927 nipype.workflow INFO:
	 [Node] Finished "21_md_7_2", elapsed time 1.31346s.
240323-15:41:00,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
240323-15:41:00,613 nipype.workflow INFO:
	 [Node] Executing "22_me_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:41:03,189 nipype.workflow INFO:
	 [Node] Finished "22_me_7_2", elapsed time 2.576308s.
240323-15:41:04,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
240323-15:41:04,612 nipype.workflow INFO:
	 [Node] Executing "23_depad_mask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:41:05,234 nipype.workflow INFO:
	 [Node] Finished "23_depad_mask", elapsed time 0.621838s.
240323-15:41:06,609 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/msk_conform".
240323-15:41:06,613 nipype.workflow INFO:
	 [Node] Executing "msk_conform" <nipype.interfaces.utility.wrappers.Function>
240323-15:41:06,801 nipype.workflow INFO:
	 [Node] Finished "msk_conform", elapsed time 0.187184s.
240323-15:41:15,364 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
240323-15:41:15,365 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:41:16,319 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 0.954324s.
Captured warning (<class 'UserWarning'>): Reference space not set
240323-15:41:19,892 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol0".
240323-15:41:19,892 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol1".
240323-15:41:19,893 nipype.workflow INFO:
	 [Node] Executing "_create_wm_distvol0" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,893 nipype.workflow INFO:
	 [Node] Executing "_create_wm_distvol1" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,894 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol1".
240323-15:41:19,895 nipype.workflow INFO:
	 [Node] Executing "_create_pial_distvol1" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,898 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol0".
240323-15:41:19,899 nipype.workflow INFO:
	 [Node] Executing "_create_pial_distvol0" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,920 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/resample".
240323-15:41:19,923 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:21,751 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.827715s.
240323-15:41:21,753 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/resample".
240323-15:41:21,757 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:22,124 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/resample".
240323-15:41:23,731 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.973246s.
240323-15:41:25,523 nipype.interface WARNING:
	 Changing /data/derivatives/smriprep/smriprep/sub-PROJECT107/ses-A/anat/sub-PROJECT107_ses-A_desc-aseg_dseg.nii.gz dtype from float32 to int16
240323-15:41:25,897 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.refine" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/refine".
240323-15:41:25,904 nipype.workflow INFO:
	 [Node] Executing "refine" <niworkflows.interfaces.freesurfer.RefineBrainMask>
240323-15:41:26,270 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:28,154 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.881231s.
240323-15:41:29,893 nipype.interface WARNING:
	 Changing /data/derivatives/smriprep/smriprep/sub-PROJECT107/ses-A/anat/sub-PROJECT107_ses-A_desc-aparcaseg_dseg.nii.gz dtype from float32 to int16
240323-15:41:58,916 nipype.workflow INFO:
	 [Node] Finished "refine", elapsed time 33.009822s.
240323-15:41:59,934 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.applyrefined" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/applyrefined".
240323-15:42:00,499 nipype.workflow INFO:
	 [Node] Executing "applyrefined" <nipype.interfaces.fsl.maths.ApplyMask>
240323-15:42:01,871 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.ds_std_volumes_wf.mask_t1w" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/ds_std_volumes_wf/mask_t1w".
240323-15:42:01,874 nipype.workflow INFO:
	 [Node] Executing "mask_t1w" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:42:03,175 nipype.workflow INFO:
	 [Node] Finished "mask_t1w", elapsed time 1.30036s.
240323-15:42:03,568 nipype.workflow INFO:
	 [Node] Finished "applyrefined", elapsed time 3.067401s.
240323-15:42:03,878 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fast" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fast".
240323-15:42:03,881 nipype.workflow INFO:
	 [Node] Executing "fast" <nipype.interfaces.fsl.preprocess.FAST>
240323-15:42:18,490 nipype.workflow INFO:
	 [Node] Finished "_create_wm_distvol0", elapsed time 58.527644s.
240323-15:42:19,514 nipype.workflow INFO:
	 [Node] Finished "_create_wm_distvol1", elapsed time 59.539599s.
240323-15:42:19,869 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol0".
240323-15:42:19,869 nipype.workflow INFO:
	 [Node] Cached "_create_wm_distvol0" - collecting precomputed outputs
240323-15:42:19,870 nipype.workflow INFO:
	 [Node] "_create_wm_distvol0" found cached.
240323-15:42:19,870 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol1".
240323-15:42:19,871 nipype.workflow INFO:
	 [Node] Cached "_create_wm_distvol1" - collecting precomputed outputs
240323-15:42:19,871 nipype.workflow INFO:
	 [Node] "_create_wm_distvol1" found cached.
240323-15:42:28,863 nipype.workflow INFO:
	 [Node] Finished "_create_pial_distvol0", elapsed time 68.885826s.
240323-15:42:30,731 nipype.workflow INFO:
	 [Node] Finished "_create_pial_distvol1", elapsed time 70.775295s.
240323-15:42:31,832 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol0".
240323-15:42:31,832 nipype.workflow INFO:
	 [Node] Cached "_create_pial_distvol0" - collecting precomputed outputs
240323-15:42:31,833 nipype.workflow INFO:
	 [Node] "_create_pial_distvol0" found cached.
240323-15:42:31,833 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol1".
240323-15:42:31,834 nipype.workflow INFO:
	 [Node] Cached "_create_pial_distvol1" - collecting precomputed outputs
240323-15:42:31,834 nipype.workflow INFO:
	 [Node] "_create_pial_distvol1" found cached.
240323-15:42:33,827 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_ribbon_wf.make_ribbon" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/make_ribbon".
240323-15:42:33,828 nipype.workflow INFO:
	 [Node] Executing "make_ribbon" <smriprep.interfaces.surf.MakeRibbon>
240323-15:42:34,438 nipype.workflow INFO:
	 [Node] Finished "make_ribbon", elapsed time 0.60952s.
240323-15:43:29,759 nipype.workflow INFO:
	 [Node] Finished "fast", elapsed time 85.877111s.
240323-15:43:29,835 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.lut_t1w_dseg" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/lut_t1w_dseg".
240323-15:43:29,837 nipype.workflow INFO:
	 [Node] Executing "lut_t1w_dseg" <nipype.interfaces.utility.wrappers.Function>
240323-15:43:30,42 nipype.workflow INFO:
	 [Node] Finished "lut_t1w_dseg", elapsed time 0.204572s.
240323-15:43:37,735 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.seg_rpt" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/seg_rpt".
240323-15:43:37,737 nipype.workflow INFO:
	 [Node] Executing "seg_rpt" <niworkflows.interfaces.reportlets.masks.ROIsPlot>
240323-15:43:55,88 nipype.workflow INFO:
	 [Node] Finished "seg_rpt", elapsed time 17.351331s.
240323-15:57:52,574 nipype.workflow INFO:
	 [Node] Finished "_msmsulc0", elapsed time 1412.860192s.
240323-15:58:02,821 nipype.workflow INFO:
	 [Node] Finished "_msmsulc1", elapsed time 1423.105562s.
240323-15:58:03,506 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.msmsulc".
240323-15:58:03,509 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] Cached "_msmsulc0" - collecting precomputed outputs
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] "_msmsulc0" found cached.
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240323-15:58:03,513 nipype.workflow INFO:
	 [Node] Cached "_msmsulc1" - collecting precomputed outputs
240323-15:58:03,513 nipype.workflow INFO:
	 [Node] "_msmsulc1" found cached.

In my current role, I do not have the throughput to bring this PR up to date. If you know anyone who would be interested in doing so, I would be happy to help.
Otherwise, I think we should drop the FastSurfer installation & interface and just add examples of using FastSurfer inputs to the relevant documentation for sMRIPrep/fMRIPrep.

Please let me know what you think! I appreciate the feedback and guidance on this.

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3 participants