Incorporating FastSurfer to sMRIPrep as surface reconstruction option
pcamach2 opened this issue · comments
Is your feature request related to a problem? Please describe.
No
Describe the solution you'd like
Addition of FastSurfer workflows as an alternative to FreeSurfer.
Describe alternatives you've considered
I have considered just running FastSurfer before running sMRIPrep or fMRIPrep and using the outputs as an existing Freesurfer output directory. This may work as discussed in #273 by @effigies.
Additional context
I brought this up in the Nipype discourse group and @oesteban suggested moving the discussion here on GitHub.
I have a working Dockerfile that includes FastSurfer and sMRIPrep, which I have used to run FastSurfer on my workstation.
Currently, building the Docker image requires having downloaded a local copy of Convert3D since my build machine was throwing errors for ca-certificates when trying to curl the tar.gz from SourceForge as part of the build. 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
I am building a Singularity image to test on our cluster and will test both tools separately before scripting this into the relevant nipype workflows.
I appreciate any help and/or feedback!
###Environment testing:###
- Complete runs of FastSurfer GPU in the Docker version of this container
- Complete runs of FastSurfer GPU in the Singularity version of this container
- Complete runs of sMRIPrep in the Docker version of this container
- Complete runs of sMRIPrep in the Singularity version of this container
###Adapting existing surfaces.py to use FastSurfer outputs as existing Freesurfer directory:###
- Attempt runs of sMRIPrep using FastSurfer outputs in the Docker version of this container (mounted surfaces.py with change committed by @effigies in #273 to /src/smriprep/smriprep/workflows/surfaces.py, mounted FastSurfer output to /opt/scratch/freesurfer, provided --fs-subjects-dir /opt/scratch/freesurfer argument in run command)
- Attempt runs of sMRIPrep using FastSurfer outputs in the Singularity version of this container (mounted surfaces.py with change committed by @effigies in #273 to /src/smriprep/smriprep/workflows/surfaces.py, mounted FastSurfer output to /opt/scratch/freesurfer, provided --fs-subjects-dir /opt/scratch/freesurfer argument in run command)
My tests have found that passing nu.mgz is not sufficient for using FastSurfer outputs as the pre-existing Freesurfer directory. As a temporary approach, I made copies of the aparc.DKTatlas+aseg.deep.mgz to it's closest relative files (aparc.DKTatlas+aseg.mgz and aparc+aseg.mgz separately and then simultaneously) and then added the flag -noaparc2aseg to the autorecon3 command in surfaces.py. This also does not successfully bypass much of the recon-all workflow.
$ docker run -it --rm --gpus all -v /path/to/PTE/bids:/data -v /path/to/singularity_images/fslicense/license.txt:/opt/freesurfer/license.txt -v /path/to/singularity_images/smriprep_dev/surfaces.py:/src/smriprep/smriprep/workflows/surfaces.py -v /path/to/PTE/bids/derivatives/fastsurfer:/opt/scratch/freesurfer smriprep:fastsurfer_dev /data/ /data/derivatives/smriprep/ --fs-subjects-dir /opt/scratch/freesurfer --fs-license-file /opt/freesurfer/license.txt participant --participant-label sub-PTE115
/opt/conda/lib/python3.8/site-packages/bids/layout/models.py:148: FutureWarning: The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
warnings.warn("The 'extension' entity currently excludes the leading dot ('.'). "
220302-02:08:35,734 nipype.workflow Level 25:
Running sMRIPrep version :
* BIDS dataset path: /data.
* Participant list: ['PTE115'].
* Run identifier: 20220302-020832_5cfef73c-51a2-4af0-a7b0-7a5f147297e4.
Spatial References: <none>.
220302-02:08:36,155 nipype.utils WARNING:
A newer version (1.7.0) of nipy/nipype is available. You are using 1.6.1
220302-02:08:43,643 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*
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.6.1
(@nipype1; @nipype2; RRID:SCR_002502).
Anatomical data preprocessing
: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@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 6.0.5.1:57b01774, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
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
220302-02:08:49,294 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.full_wm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/full_wm".
220302-02:08:49,303 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_norm_wf/outputnode".
220302-02:08:49,304 nipype.workflow INFO:
[Node] Running "full_wm" ("nipype.interfaces.utility.wrappers.Function")
220302-02:08:49,310 nipype.workflow INFO:
[Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
220302-02:08:49,401 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_norm_wf.outputnode".
220302-02:08:49,668 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
220302-02:08:49,672 nipype.workflow INFO:
[Node] Running "lap_tmpl" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1
220302-02:08:49,713 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
220302-02:08:49,716 nipype.workflow INFO:
[Node] Running "res_tmpl" ("niworkflows.interfaces.nibabel.RegridToZooms")
220302-02:08:50,393 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.full_wm".
220302-02:08:51,919 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl".
220302-02:08:52,811 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.bidssrc" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/bidssrc".
220302-02:08:52,818 nipype.workflow INFO:
[Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
220302-02:08:52,881 nipype.interface INFO:
No "bold" images found for sub-<undefined>
220302-02:08:52,881 nipype.interface INFO:
No "t2w" images found for sub-<undefined>
220302-02:08:52,881 nipype.interface INFO:
No "sbref" images found for sub-<undefined>
220302-02:08:52,881 nipype.interface INFO:
No "roi" images found for sub-<undefined>
220302-02:08:52,889 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.bidssrc".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220302-02:08:55,47 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
220302-02:08:56,684 nipype.utils WARNING:
A newer version (1.7.0) of nipy/nipype is available. You are using 1.6.1
220302-02:08:56,814 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.fs_isrunning" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/fs_isrunning".
220302-02:08:58,750 nipype.workflow INFO:
[Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
220302-02:08:58,863 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions".
220302-02:09:00,546 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
220302-02:09:00,620 nipype.workflow INFO:
[Node] Running "fs_isrunning" ("nipype.interfaces.utility.wrappers.Function")
220302-02:09:00,702 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.fs_isrunning".
220302-02:09:00,859 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.t1w_conform" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_template_wf/t1w_conform".
220302-02:09:00,865 nipype.workflow INFO:
[Node] Setting-up "_t1w_conform0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0".
220302-02:09:00,867 nipype.workflow INFO:
[Node] Running "_t1w_conform0" ("niworkflows.interfaces.images.Conform")
220302-02:09:00,955 nipype.workflow INFO:
[Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function")
220302-02:09:00,962 nipype.workflow INFO:
[Node] Finished "_t1w_conform0".
220302-02:09:00,964 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.t1w_conform".
220302-02:09:01,24 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources".
220302-02:09:02,406 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl".
220302-02:09:02,462 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.get1st" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/anat_template_wf/get1st".
220302-02:09:02,937 nipype.workflow INFO:
[Node] Running "get1st" ("nipype.interfaces.utility.base.Select")
220302-02:09:03,18 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.anat_template_wf.get1st".
220302-02:09:04,477 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl".
220302-02:09:04,898 nipype.workflow INFO:
[Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge")
220302-02:09:04,982 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl".
220302-02:09:06,482 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/fov_check".
220302-02:09:06,911 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/truncate_images".
220302-02:09:06,921 nipype.workflow INFO:
[Node] Setting-up "_truncate_images0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
220302-02:09:06,925 nipype.workflow INFO:
[Node] Running "_truncate_images0" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_maths.nii.gz TruncateImageIntensity /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz 0.01 0.999 256
220302-02:09:06,946 nipype.workflow INFO:
[Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
220302-02:09:07,736 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.fov_check".
220302-02:09:11,447 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/recon_config".
220302-02:09:12,13 nipype.workflow INFO:
[Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
220302-02:09:12,131 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.recon_config".
220302-02:09:15,890 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
220302-02:09:17,489 nipype.interface INFO:
resume recon-all : recon-all -autorecon1 -FLAIR /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_FLAIR.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -expert /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220302-02:09:17,489 nipype.workflow INFO:
[Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -FLAIR /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_FLAIR.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -expert /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220302-02:09:17,553 nipype.interface INFO:
resume recon-all : recon-all -autorecon1 -FLAIR /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_FLAIR.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -expert /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220302-02:09:28,7 nipype.workflow INFO:
[Node] Finished "_truncate_images0".
220302-02:09:28,10 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.truncate_images".
220302-02:09:28,871 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4".
220302-02:09:28,881 nipype.workflow INFO:
[Node] Setting-up "_inu_n40" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
220302-02:09:28,886 nipype.workflow INFO:
[Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-PTE115_ses-A_T1w_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-PTE115_ses-A_T1w_maths_corrected.nii.gz --shrink-factor 4
220302-02:10:46,793 nipype.workflow INFO:
[Node] Finished "_inu_n40".
220302-02:10:46,798 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.inu_n4".
220302-02:10:48,981 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/lap_target".
220302-02:10:48,987 nipype.workflow INFO:
[Node] Running "lap_target" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_maths_corrected_maths.nii.gz Laplacian /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-PTE115_ses-A_T1w_maths_corrected.nii.gz 1.5 1
220302-02:10:49,47 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/res_target".
220302-02:10:49,117 nipype.workflow INFO:
[Node] Running "res_target" ("niworkflows.interfaces.nibabel.RegridToZooms")
220302-02:10:52,193 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.res_target".
220302-02:10:52,942 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/init_aff".
220302-02:10:53,65 nipype.workflow INFO:
[Node] Running "init_aff" ("nipype.interfaces.ants.utils.AI"), a CommandLine Interface with command:
antsAI -c [10,1e-06,10] -d 3 -x /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_regrid.nii.gz,/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-PTE115_ses-A_T1w_maths_corrected_regrid.nii.gz,32,Regular,0.25] -o initialization.mat -p 0 -s [15,0.1] -g [40.0,0x40x40] -t Affine[0.1] -v 1
220302-02:11:12,138 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.lap_target".
220302-02:11:12,588 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/mrg_target".
220302-02:11:12,956 nipype.workflow INFO:
[Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge")
220302-02:11:13,26 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.mrg_target".
220302-02:11:23,442 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.init_aff".
220302-02:11:25,18 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/norm".
220302-02:11:25,35 nipype.workflow INFO:
[Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-PTE115_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-PTE115_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-PTE115_ses-A_T1w_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-PTE115_ses-A_T1w_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 0
220302-02:12:21,795 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
220302-02:12:27,592 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm".
220302-02:12:28,223 nipype.workflow INFO:
[Node] Running "fsnative2t1w_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /opt/scratch/freesurfer/sub-PTE115/mri/T1.mgz --dst /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz
220302-02:13:35,656 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm".
Captured warning (<class 'UserWarning'>): Reference space not set
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220302-02:13:41,850 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm".
220302-02:13:41,855 nipype.workflow INFO:
[Node] Running "t1w2fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --invert --outlta /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta
220302-02:13:42,59 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm".
220302-02:23:57,421 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.norm".
220302-02:23:59,887 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask".
220302-02:23:59,892 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask".
220302-02:23:59,915 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /home/smriprep/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz --transform [ /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220302-02:23:59,915 nipype.workflow INFO:
[Node] Running "map_wmmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/full_wm/summap.nii.gz --interpolation Gaussian --output summap_trans.nii.gz --reference-image /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz --transform [ /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220302-02:25:20,578 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask".
220302-02:25:21,496 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask".
220302-02:25:21,598 nipype.workflow INFO:
[Node] Running "thr_brainmask" ("nipype.interfaces.ants.utils.ThresholdImage"), a CommandLine Interface with command:
ThresholdImage 3 /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000
220302-02:25:24,516 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask".
220302-02:25:24,661 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask".
220302-02:25:25,537 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
220302-02:25:25,538 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final".
220302-02:25:25,542 nipype.workflow INFO:
[Node] Running "03_pad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10
220302-02:25:25,547 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
220302-02:25:25,553 nipype.workflow INFO:
[Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-PTE115_ses-A_T1w_corrected.nii.gz, sub-PTE115_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask/summap_trans.nii.gz
220302-02:25:25,653 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
220302-02:25:25,658 nipype.workflow INFO:
[Node] Running "dil_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2
220302-02:25:28,95 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask".
220302-02:25:29,803 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask".
220302-02:25:31,598 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask".
220302-02:25:31,603 nipype.workflow INFO:
[Node] Running "get_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220302-02:25:36,230 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask".
220302-02:26:12,419 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0".
220302-02:26:12,422 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final".
220302-02:26:13,533 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/apply_mask".
220302-02:26:13,538 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
220302-02:26:13,541 nipype.workflow INFO:
[Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220302-02:26:13,582 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos".
220302-02:26:13,590 nipype.workflow INFO:
[Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command:
Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-PTE115_ses-A_T1w_corrected.nii.gz --likelihood-model Gaussian --mask-image /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-PTE115_ses-A_T1w_corrected_labeled.nii.gz,POSTERIOR_%02d.nii.gz] --use-random-seed 1
220302-02:26:15,151 nipype.workflow INFO:
[Node] Finished "_apply_mask0".
220302-02:26:15,154 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.apply_mask".
220302-02:28:42,717 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos".
220302-02:28:43,681 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
220302-02:28:43,703 nipype.workflow INFO:
[Node] Running "02_pad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-PTE115_ses-A_T1w_corrected_labeled.nii.gz 10
220302-02:28:46,112 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm".
220302-02:28:51,566 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
220302-02:28:51,634 nipype.workflow INFO:
[Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function")
220302-02:28:52,485 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels".
220302-02:28:53,571 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm".
220302-02:28:53,572 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf".
220302-02:28:53,572 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
220302-02:28:53,577 nipype.workflow INFO:
[Node] Running "05_get_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-03.nii.gz
220302-02:28:53,577 nipype.workflow INFO:
[Node] Running "10_me_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz ME /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz 10
220302-02:28:53,580 nipype.workflow INFO:
[Node] Running "27_depad_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz -10
220302-02:28:53,635 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm".
220302-02:28:53,640 nipype.workflow INFO:
[Node] Running "06_get_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02.nii.gz
220302-02:28:55,429 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf".
220302-02:28:55,560 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
220302-02:28:55,681 nipype.workflow INFO:
[Node] Running "apply_wm_prior" ("nipype.interfaces.utility.wrappers.Function")
220302-02:28:57,776 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior".
220302-02:28:57,815 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm".
220302-02:28:58,87 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm".
220302-02:28:59,578 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
220302-02:28:59,578 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
220302-02:28:59,582 nipype.workflow INFO:
[Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz
220302-02:28:59,583 nipype.workflow INFO:
[Node] Running "07_fill_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz 2
220302-02:28:59,583 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final".
220302-02:28:59,591 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
220302-02:28:59,597 nipype.workflow INFO:
[Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-PTE115/ses-A/anat/sub-PTE115_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-PTE115_ses-A_T1w_corrected.nii.gz, sub-PTE115_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior/prodmap.nii.gz
220302-02:29:02,18 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm".
220302-02:29:03,586 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
220302-02:29:03,592 nipype.workflow INFO:
[Node] Running "26_depad_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10
220302-02:29:06,291 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm".
220302-02:29:06,498 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf".
220302-02:29:27,150 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm".
220302-02:29:27,589 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
220302-02:29:27,595 nipype.workflow INFO:
[Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz
220302-02:29:30,548 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm".
220302-02:29:31,591 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm".
220302-02:29:31,597 nipype.workflow INFO:
[Node] Running "11_add_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 08_mult_gm_maths.nii.gz addtozero /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-PTE115_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz
220302-02:29:40,866 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm".
220302-02:29:41,601 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
220302-02:29:41,616 nipype.workflow INFO:
[Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz
220302-02:29:44,419 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm".
220302-02:29:45,606 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
220302-02:29:45,606 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
220302-02:29:45,611 nipype.workflow INFO:
[Node] Running "25_depad_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10
220302-02:29:45,611 nipype.workflow INFO:
[Node] Running "13_add_gm_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz
220302-02:29:45,952 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0".
220302-02:29:45,955 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final".
220302-02:29:47,839 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm".
220302-02:29:49,624 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms".
220302-02:29:49,635 nipype.workflow INFO:
[Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge")
220302-02:29:49,642 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms".
220302-02:29:55,573 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm".
220302-02:29:57,635 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
220302-02:29:57,635 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
220302-02:29:57,642 nipype.workflow INFO:
[Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function")
220302-02:29:57,643 nipype.workflow INFO:
[Node] Running "24_depad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10
220302-02:29:58,281 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2".
220302-02:29:59,634 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7".
220302-02:29:59,647 nipype.workflow INFO:
[Node] Running "15_add_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz
220302-02:30:00,382 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm".
220302-02:30:07,562 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7".
220302-02:30:09,649 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7".
220302-02:30:09,657 nipype.workflow INFO:
[Node] Running "16_me_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2
220302-02:30:17,304 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7".
220302-02:30:17,656 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7".
220302-02:30:17,667 nipype.workflow INFO:
[Node] Running "17_comp_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz
220302-02:30:22,161 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7".
220302-02:30:23,728 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7".
220302-02:30:23,734 nipype.workflow INFO:
[Node] Running "18_md_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4
220302-02:30:28,277 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7".
220302-02:30:29,667 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7".
220302-02:30:29,675 nipype.workflow INFO:
[Node] Running "19_fill_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2
220302-02:30:52,393 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7".
220302-02:30:53,751 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
220302-02:30:53,760 nipype.workflow INFO:
[Node] Running "20_add_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220302-02:31:02,753 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2".
220302-02:31:03,710 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
220302-02:31:03,720 nipype.workflow INFO:
[Node] Running "21_md_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5
220302-02:31:08,707 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2".
220302-02:31:09,716 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
220302-02:31:09,722 nipype.workflow INFO:
[Node] Running "22_me_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5
220302-02:31:17,5 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2".
220302-02:31:17,713 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
220302-02:31:17,723 nipype.workflow INFO:
[Node] Running "23_depad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10
220302-02:31:20,104 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask".
220302-02:31:21,732 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform".
220302-02:31:21,867 nipype.workflow INFO:
[Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function")
220302-02:31:22,419 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform".
220302-02:31:34,632 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220302-02:31:34,640 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
220302-02:31:34,646 nipype.workflow INFO:
[Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220302-02:31:36,310 nipype.workflow INFO:
[Node] Finished "_apply_mask0".
220302-02:31:36,313 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask".
220302-02:31:43,4 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
220302-02:31:43,503 nipype.workflow INFO:
[Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
220302-02:31:47,301 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
220302-02:31:52,195 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
220302-02:31:53,782 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220302-02:31:53,783 nipype.workflow INFO:
[Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220302-02:31:53,785 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220302-04:39:08,768 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
220302-04:39:10,896 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220302-04:39:10,917 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-04:39:10,917 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-04:39:10,921 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-04:39:14,626 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220302-04:39:14,640 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-04:39:14,641 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-04:39:14,644 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nopial -nopctsurfcon
220302-05:25:27,430 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
220302-05:28:10,189 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
220302-05:28:11,938 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
220302-05:28:11,956 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220302-05:28:11,970 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:11,970 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220302-05:28:11,975 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:12,95 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
220302-05:28:12,103 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220302-05:28:12,125 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:12,126 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220302-05:28:12,130 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:12,251 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
220302-05:28:12,260 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
220302-05:28:13,931 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
220302-05:28:13,945 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:13,945 nipype.workflow INFO:
[Node] Running "cortribbon" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220302-05:28:13,948 nipype.interface INFO:
recon-all complete : Not running
220302-05:28:14,129 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon".
220302-05:28:18,504 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220302-05:28:18,511 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:28:18,512 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:28:18,514 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:28:21,839 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220302-05:28:21,846 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:28:21,847 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:28:21,850 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220302-05:35:47,609 nipype.workflow INFO:
[Node] Finished "_parcstats1".
220302-05:35:55,266 nipype.workflow INFO:
[Node] Finished "_parcstats0".
220302-05:35:59,666 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
220302-05:35:59,676 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220302-05:35:59,689 nipype.interface INFO:
recon-all complete : Not running
220302-05:35:59,690 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220302-05:35:59,693 nipype.interface INFO:
recon-all complete : Not running
220302-05:35:59,807 nipype.workflow INFO:
[Node] Finished "_parcstats0".
220302-05:35:59,814 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220302-05:35:59,858 nipype.interface INFO:
recon-all complete : Not running
220302-05:35:59,858 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220302-05:35:59,862 nipype.interface INFO:
recon-all complete : Not running
220302-05:35:59,952 nipype.workflow INFO:
[Node] Finished "_parcstats1".
220302-05:35:59,960 nipype.workflow INFO:
[Node] Finished "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
220302-05:36:03,837 nipype.workflow INFO:
[Node] Setting-up "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
220302-05:36:03,846 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -nosegstats -nobalabels
220302-05:36:03,847 nipype.workflow INFO:
[Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -nosegstats -nobalabels
220302-05:36:03,850 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -nosegstats -nobalabels
220302-05:36:48,394 nipype.workflow WARNING:
Storing result file without outputs
220302-05:36:48,395 nipype.workflow WARNING:
[Node] Error on "smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" (/tmp/work/smriprep_wf/single_subject_PTE115_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3)
220302-05:36:50,318 nipype.workflow ERROR:
Node autorecon3 failed to run on host 199390e9ab0c.
220302-05:36:50,502 nipype.workflow ERROR:
Saving crash info to /data/derivatives/smriprep/smriprep/sub-PTE115/log/20220302-020832_5cfef73c-51a2-4af0-a7b0-7a5f147297e4/crash-20220302-053650-root-autorecon3-a0e47803-7acb-420d-a52a-2e6b4c8644ee.txt
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
recon-all -autorecon3 -openmp 8 -subjid sub-PTE115 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -nosegstats -nobalabels
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /opt/scratch/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rwxrwxr-x 1 357608 62046 384676 Mar 2 04:39 /opt/scratch/freesurfer/sub-PTE115/scripts/recon-all.log
Linux 199390e9ab0c 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/opt/scratch/freesurfer/sub-PTE115/scripts/recon-all.local-copy'
#-----------------------------------------
#@# AParc-to-ASeg aparc Wed Mar 2 05:36:05 UTC 2022
/opt/scratch/freesurfer/sub-PTE115
mri_aparc2aseg --s sub-PTE115 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /opt/scratch/freesurfer
subject sub-PTE115
outvol /opt/scratch/freesurfer/sub-PTE115/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/opt/scratch/freesurfer/sub-PTE115/surf/lh.white
Reading lh pial surface
/opt/scratch/freesurfer/sub-PTE115/surf/lh.pial
Loading lh annotations from /opt/scratch/freesurfer/sub-PTE115/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface
/opt/scratch/freesurfer/sub-PTE115/surf/rh.white
Reading rh pial surface
/opt/scratch/freesurfer/sub-PTE115/surf/rh.pial
Loading rh annotations from /opt/scratch/freesurfer/sub-PTE115/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /opt/scratch/freesurfer/sub-PTE115/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /opt/scratch/freesurfer/sub-PTE115/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mri_aparc2aseg: could not read mri/aseg.auto_noCCseg.label_intensities.txt
-------------------------
Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.19
No such file or directory
Linux 199390e9ab0c 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-PTE115 exited with ERRORS at Wed Mar 2 05:36:48 UTC 2022
For more details, see the log file /opt/scratch/freesurfer/sub-PTE115/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
220302-05:36:52,315 nipype.workflow ERROR:
could not run node: smriprep_wf.single_subject_PTE115_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3
Preprocessing did not finish successfully. Errors occurred while processing data from participants: PTE115 (1). Check the HTML reports for details.
###Creating shippable code:###
- Build FastSurfer version of surfaces.py
- Build FastSurfer option into relevant Nipype workflows
- Test on Docker
- Test on Singularity
Any help with integrating this to Nipype would be very much appreciated!
Hi @pcamach2, thanks for this!
To create a nipype interface for FastSurfer, we're going to need to know a few things:
- What does a command-line look like? What inputs does it have, what options does it have?
- Is there a notion of resuming, as there is in FreeSurfer? Do we need to include machinery to detect partially complete runs?
Hi @effigies, no problem!
Here is what I have so far:
1. What does a command-line look like? What inputs does it have, what options does it have?
Per the basic FastSurfer container run instructions, the barebones docker run command is as follows for their Docker image:
docker run --gpus all -v /home/user/my_mri_data:/data \
-v /home/user/my_fastsurfer_analysis:/output \
-v /home/user/my_fs_license_dir:/fs60 \
--rm --user XXXX fastsurfer:gpu \
--fs_license /fs60/.license \
--t1 /data/subject2/orig.mgz \
--sid subject2 --sd /output \
--parallel
From the hybrid container that I built, my tests ran with the following (with all replaced with actual labels from the test dataset):
For the Singularity container (running from the project directory):
singularity exec --nv -B ./bids:/data,./bids/derivatives/fastsurfer:/output,/path/to/freesurferlicense/license.txt:/fs60/license \
/path/to/smriprep-fastsurfer_dev.sif /opt/FastSurfer/run_fastsurfer.sh --fs_license /fs60/license \
--t1 /data/sub-<label>/ses-<label>/anat/sub-<label>_ses-<label>_T1w.nii.gz --sid sub-<label> --sd /output
From the shell in the container:
/opt/FastSurfer/run_fastsurfer.sh --fs_license /fs60/license \
--t1 /data/sub-<label>/ses-<label>/anat/sub-<label>_ses-<label>_acq-<label>_T1w.nii.gz \
--sid sub-<label> --sd /output
Note that the FreeSurfer license is mounted to /fs60/license - this is just their convention for mounting.
This project was not set up for the new BIDS specification, so these "raw" BIDS NIFTIs should be in project/bids/sourcedata now.
The full list of arguments is explained as follows:
--sd: Output directory $SUBJECTS_DIR (equivalent to FreeSurfer setup --> $SUBJECTS_DIR/sid/mri; $SUBJECTS_DIR/sid/surf ... will be created).
--sid: Subject ID for directory inside $SUBJECTS_DIR to be created ($SUBJECTS_DIR/sid/...)
--t1: T1 full head input (not bias corrected, global path). The network was trained with conformed images (UCHAR, 256x256x256, 1 mm voxels and standard slice orientation). These specifications are checked in the eval.py script and the image is automatically conformed if it does not comply.
--fs_license: Path to FreeSurfer license key file. Register (for free) at https://surfer.nmr.mgh.harvard.edu/registration.html to obtain it if you do not have FreeSurfer installed so far. Strictly necessary if you use Docker, optional for local install (your local FreeSurfer license will automatically be used)
Network specific arguments (optional):
--seg: Global path with filename of segmentation (where and under which name to store it). Default location: $SUBJECTS_DIR/$sid/mri/aparc.DKTatlas+aseg.deep.mgz
--weights_sag: Pretrained weights of sagittal network. Default: ../checkpoints/Sagittal_Weights_FastSurferCNN/ckpts/Epoch_30_training_state.pkl
--weights_ax: Pretrained weights of axial network. Default: ../checkpoints/Axial_Weights_FastSurferCNN/ckpts/Epoch_30_training_state.pkl
--weights_cor: Pretrained weights of coronal network. Default: ../checkpoints/Coronal_Weights_FastSurferCNN/ckpts/Epoch_30_training_state.pkl
--seg_log: Name and location for the log-file for the segmentation (FastSurferCNN). Default: $SUBJECTS_DIR/$sid/scripts/deep-seg.log
--clean_seg: Flag to clean up FastSurferCNN segmentation
--run_viewagg_on: Define where the view aggregation should be run on. By default, the program checks if you have enough memory to run the view aggregation on the gpu. The total memory is considered for this decision. If this fails, or you actively overwrote the check with setting "--run_viewagg_on cpu", view agg is run on the cpu. Equivalently, if you define "--run_viewagg_on gpu", view agg will be run on the gpu (no memory check will be done).
--no_cuda: Flag to disable CUDA usage in FastSurferCNN (no GPU usage, inference on CPU)
--batch: Batch size for inference. Default: 16. Lower this to reduce memory requirement
--order: Order of interpolation for mri_convert T1 before segmentation (0=nearest, 1=linear(default), 2=quadratic, 3=cubic)
Surface pipeline arguments (optional):
--fstess: Use mri_tesselate instead of marching cube (default) for surface creation
--fsqsphere: Use FreeSurfer default instead of novel spectral spherical projection for qsphere
--fsaparc: Use FS aparc segmentations in addition to DL prediction (slower in this case and usually the mapped ones from the DL prediction are fine)
--surfreg: Create Surface-Atlas (sphere.reg) registration with FreeSurfer (for cross-subject correspondence or other mappings)
--parallel: Run both hemispheres in parallel
--threads: Set openMP and ITK threads to
Other:
--py: which python version to use. Default: python3.6
--seg_only: only run FastSurferCNN (generate segmentation, do not run the surface pipeline)
--surf_only: only run the surface pipeline recon_surf. The segmentation created by FastSurferCNN must already exist in this case.
I think the most important factor that we would need to consider is whether folks are running with GPU or CPU since this could affect the image they would use. One way to handle that would be building separate versions and tag them with "GPU" or "CPU" accordingly. Otherwise, I think we can build the general GPU version by default and allow the --no_cuda argument to handle this.
2. Is there a notion of resuming, as there is in FreeSurfer? Do we need to include machinery to detect partially complete runs?
I haven't had to quit and resume with FastSurfer due to the shorter run time and the lack of long process stalling that can occur in recon-all, so I can't say from experience.
The main breakpoint built in is that the segmentation via CNN can be run standalone and then followed by surface reconstruction. I have not personally taken this approach, but it might be useful if someone wants to generate a large batch of segmentations and check them before committing to surface reconstruction (although it seems more likely that they would just use standalone FastSurfer in this use case).
I would lean towards using a fresh run if all output files are not detected; this also makes it easier to assess quality with their adapted QATools, which NaNs out when the recon-all log indicates restarts.
For reference, here are the example outputs from a bids/derivatives/fastsurfer/sub- directory:
./bids/derivatives/fastsurfer/sub-<label>/label:
aparc.annot.mapped.ctab
lh.aparc.mapped.annot
lh.aparc.mapped.prefix.annot
lh.cortex.label
rh.aparc.mapped.annot
rh.aparc.mapped.prefix.annot
rh.cortex.label
./bids/derivatives/fastsurfer/sub-<label>/mri:
aparc+aseg.orig.mgz
aparc.DKTatlas+aseg.deep.mgz
aparc.DKTatlas+aseg.deep.withCC.mgz
aparc.mapped+aseg.mgz
aseg.auto.mgz
aseg.auto_noCCseg.mgz
aseg.mgz
aseg.presurf.hypos.mgz
aseg.presurf.mgz
brain.finalsurfs.mgz
brainmask.mgz
brain.mgz
filled.mgz
filled-pretess127.mgz
filled-pretess255.mgz
lh.ribbon.mgz
mask.mgz
mri_nu_correct.mni.log
mri_nu_correct.mni.log.bak
norm.mgz
nu.mgz
orig
orig.mgz
orig_nu.mgz
rawavg.mgz
rh.ribbon.mgz
ribbon.mgz
segment.dat
T1.mgz
tmp
transforms
wm.asegedit.mgz
wm.mgz
wmparc.mapped.mgz
wm.seg.mgz
./bids/derivatives/fastsurfer/sub-<label>/scripts:
build-stamp.txt
deep-seg.log
lastcall.build-stamp.txt
lh.processing.cmdf
patchdir.txt
pctsurfcon.log
pctsurfcon.log.old
ponscc.cut.log
recon-all.cmd
recon-all.done
recon-all.env
recon-all.env.bak
recon-all.local-copy
recon-all.log
recon-all-status.log
recon-surf.done
recon-surf.log
recon-surf_times.yaml
rh.processing.cmdf
./bids/derivatives/fastsurfer/sub-<label>/stats:
aseg.presurf.hypos.stats
aseg.stats
lh.aparc.mapped.stats
lh.curv.stats
lh.w-g.pct.stats
rh.aparc.mapped.stats
rh.curv.stats
rh.w-g.pct.stats
wmparc.mapped.stats
./bids/derivatives/fastsurfer/sub-<label>/surf:
lh.area
lh.area.mid
lh.area.pial
lh.curv
lh.curv.pial
lh.defect_borders
lh.defect_chull
lh.defect_labels
lh.inflated
lh.inflated.H
lh.inflated.K
lh.inflated.nofix
lh.orig
lh.orig.nofix
lh.pial
lh.qsphere.nofix
lh.smoothwm
lh.smoothwm.BE.crv
lh.smoothwm.C.crv
lh.smoothwm.FI.crv
lh.smoothwm.H.crv
lh.smoothwm.K1.crv
lh.smoothwm.K2.crv
lh.smoothwm.K.crv
lh.smoothwm.nofix
lh.smoothwm.S.crv
lh.sulc
lh.thickness
lh.volume
lh.w-g.pct.mgh
lh.white
lh.white.H
lh.white.K
lh.white.preaparc
lh.white.preaparc.H
lh.white.preaparc.K
rh.area
rh.area.mid
rh.area.pial
rh.curv
rh.curv.pial
rh.defect_borders
rh.defect_chull
rh.defect_labels
rh.inflated
rh.inflated.H
rh.inflated.K
rh.inflated.nofix
rh.orig
rh.orig.nofix
rh.pial
rh.qsphere.nofix
rh.smoothwm
rh.smoothwm.BE.crv
rh.smoothwm.C.crv
rh.smoothwm.FI.crv
rh.smoothwm.H.crv
rh.smoothwm.K1.crv
rh.smoothwm.K2.crv
rh.smoothwm.K.crv
rh.smoothwm.nofix
rh.smoothwm.S.crv
rh.sulc
rh.thickness
rh.volume
rh.w-g.pct.mgh
rh.white
rh.white.H
rh.white.K
rh.white.preaparc
rh.white.preaparc.H
rh.white.preaparc.K
./bids/derivatives/fastsurfer/sub-<label>/tmp:
./bids/derivatives/fastsurfer/sub-<label>/touch:
asegmerge.touch
cortical_ribbon.touch
fill.touch
inorm2.touch
lh.curvstats.touch
lh.inflate1.touch
lh.inflate2.touch
lh.inflate.H.K.touch
lh.smoothwm2.touch
lh.surfvolume.touch
lh.topofix.touch
lh.white.H.K.touch
relabelhypos.touch
rh.curvstats.touch
rh.inflate1.touch
rh.inflate2.touch
rh.inflate.H.K.touch
rh.smoothwm2.touch
rh.surfvolume.touch
rh.topofix.touch
rh.white.H.K.touch
rusage.mris_fix_topology.lh.dat
rusage.mris_fix_topology.rh.dat
rusage.mris_inflate.lh.dat
rusage.mris_inflate.rh.dat
segstats.touch
wmsegment.touch
./bids/derivatives/fastsurfer/sub-<label>/trash:
Thank you!
@effigies, the fix of running touch on the mri/aseg.auto_noCCseg.label_intensities.txt file (Deep-MI/FastSurfer#21 (comment)) resolves the error and allows sMRIPrep to complete.
I added a short python function to my fork of smriprep/smriprep/utils/misc.py (https://github.com/pcamach2/smriprep/blob/1377f4c629542ba8d3ab11f90b9c593ffa29b6cc/smriprep/utils/misc.py) that checks for FastSurfer files in the --fs-subjects-dir (there are .mgz files with 'deep' in the subject's mri directory, which indicate that they were generated using the deep-learning method used in FastSurfer). If detected, this function runs the touch fix and sets a fastsurfer_bool variable to 'True'.
I think the next step would be to use the fastsurfer_bool variable in anatomical.py to run minimal Freesurfer commands, but I would appreciate any advice on where best to call the check_fastsurfer function and whether I should create a separate FastSurfer-specific workflow in surfaces.py.
Thank you!
I removed the fastsurfer_bool variable and added the check_fastsurfer function to anatomical.py (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch/smriprep/workflows/anatomical.py), which successfully builds the anat workflow and touches the label_intensities file. This runs as expected, so the failure to complete when using FastSurfer outputs as --fs-subjects-dir appears to be resolved.
The next steps I can think of are:
- setting up the alternative workflow with minimal Freesurfer commands
- building a nipype FastSurfer wrapper (might need refinement)
- add FastSurfer wrapper command to anatomical.py and/or surfaces.py
- adjusting documentation and boilerplate to reflect FastSurfer being used
- adding a FastSurfer argument to the smriprep cli
@effigies, I am trying to connect the FastSurfer interface that I wrote and tested (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch-dev/smriprep/interfaces/fastsurfer.py) into the overall sMRIPrep workflow.
I added 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.",
)
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).
Thank you again for all your help and advice!
@pcamach2 Could you go ahead and open a draft PR with your changes? I think it will make it easier to look through this. Unfortunately I'm out of time today, but I'll put you on my todo list for tomorrow.