Fmriprep crash wf.initial_boldref_wf.enhance_and_skullstrip_bold_wf.n4_correct

Software Support
41

Chris, any chance you could at least provide a dockerfile that would produce a 23.0.2-fixed that solves this problem? I have one user who has hundreds of subjects processed in 23.0.2 and just ONE that is crashing with this problem, and I’d love for them to be able to finish up.

1 Like
42

I haven’t tested this, but you could try GitHub - effigies/fmriprep at docker/antspatch/23.0.x. If you clone the repository and make sure you have the 23.0.2 tag, then it should build an image that reports its version as 23.0.3.dev1+g1f4600b8. The boilerplate should also advertise that it used ANTs 2.4.4.

44

Running “make docker-build tag=23.0.2” at tags/23.0.2 (60f7066) yields:


Unpacking multiarch-support (2.27-3ubuntu1.5) ...
Setting up multiarch-support (2.27-3ubuntu1.5) ...
dpkg-deb: error: '/tmp/libxp6.deb' is not a Debian format archive
dpkg: error processing archive /tmp/libxp6.deb (--install):
 dpkg-deb --control subprocess returned error exit status 2
Errors were encountered while processing:
 /tmp/libxp6.deb
The command '/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ed            gsl-bin            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg62            libpng12-0            libxm4            netpbm            tcsh            xfonts-base            xvfb     && apt-get clean     && rm -rf /var/lib/apt/lists/*     && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb     && dpkg -i /tmp/multiarch.deb     && rm /tmp/multiarch.deb     && curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb     && dpkg -i /tmp/libxp6.deb     && rm /tmp/libxp6.deb     && apt-get install -f     && apt-get clean     && rm -rf /var/lib/apt/lists/*     && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')"     && if [ -n "$gsl2_path" ]; then          ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0";     fi     && ldconfig     && echo "Downloading AFNI ..."     && mkdir -p /opt/afni-latest     && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1     --exclude "linux_openmp_64/*.gz"     --exclude "linux_openmp_64/funstuff"     --exclude "linux_openmp_64/shiny"     --exclude "linux_openmp_64/afnipy"     --exclude "linux_openmp_64/lib/RetroTS"     --exclude "linux_openmp_64/meica.libs"     && find /opt/afni-latest -type f -not \(         -name "3dTshift" -or         -name "3dUnifize" -or         -name "3dAutomask" -or         -name "3dvolreg" \) -delete' returned a non-zero code: 1
make: *** [Makefile:14: docker-build] Error 1
45

Right. I guess we’ve been depending on cached layers for a bit. I also can’t build it locally, even pulling nipreps/docker:23.0.2 first. The simplest thing is probably just to drop this Dockerfile in an empty directory:

FROM nipreps/fmriprep:23.0.2

ENV ANTSPATH="/opt/ants" \
    PATH="/opt/ants/bin:$PATH" \
    LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
RUN rm -r /opt/ants && \
    curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.4.4/ants-2.4.4-ubuntu-22.04-X64-gcc.zip" && \
    unzip ants-2.4.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
    rm ants-2.4.4-ubuntu-22.04-X64-gcc.zip && \
    mv /opt/ants-2.4.4 /opt/ants

Then run:

docker build -t fmriprep:patch .

I did test building that one, but not running it.

1 Like
46

It doesn’t run at all:


230617-23:06:45,896 cli INFO:
         Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
230617-23:06:45,896 cli INFO:
         Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.8.0

        1: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)

        Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.


        Summary:                Available Tasks:        Available Modalities:
        19 Files, 3.68GB                                MRI
        1 - Subject
        1 - Session


        If you have any questions, please post on https://neurostars.org/tags/bids.

230617-23:07:04,587 nipype.workflow IMPORTANT:
         Running fMRIPrep version 23.0.2

         License NOTICE ##################################################
         fMRIPrep 23.0.2
         Copyright 2023 The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
230617-23:07:04,667 nipype.workflow IMPORTANT:
         Building fMRIPrep's workflow:
           * BIDS dataset path: /data/belleau_lab/TeenStress/E13347949.
           * Participant list: ['TS028'].
           * Run identifier: 20230617-230634_d5e872b5-0de0-4c1e-9489-f997db977b77.
           * Output spaces: MNI152NLin6Asym:res-2 anat fsaverage:den-164k.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /data/belleau_lab/TeenStress/E13347949/derivatives/sourcedata/freesurfer.
230617-23:07:09,446 nipype.workflow INFO:
         B0 field inhomogeneity map will be estimated with  the following 2 estimators: [<EstimatorType.ANAT: 5>, <EstimatorType.ANAT: 5>].
230617-23:07:09,998 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-EMIST_run-01_bold.nii.gz.
230617-23:07:09,999 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00001> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-EMIST_run-01_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:10,234 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.954s.
230617-23:07:10,919 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-HMIST_run-01_bold.nii.gz.
230617-23:07:10,920 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00001> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-HMIST_run-01_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:11,145 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.954s.
230617-23:07:11,481 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-HMIST_run-02_bold.nii.gz.
230617-23:07:11,481 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00001> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-HMIST_run-02_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:11,681 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.955s.
230617-23:07:12,5 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-rest_run-01_bold.nii.gz.
230617-23:07:12,5 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-rest_run-01_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:12,229 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.335s.
230617-23:07:12,572 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-rest_run-02_bold.nii.gz.
230617-23:07:12,572 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-rest_run-02_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:12,941 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.335s.
230617-23:07:13,255 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-rest_run-03_bold.nii.gz.
230617-23:07:13,255 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-rest_run-03_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:13,450 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.335s.
230617-23:07:13,766 nipype.workflow INFO:
         No single-band-reference found for sub-TS028_task-rest_run-04_bold.nii.gz.
230617-23:07:13,766 nipype.workflow INFO:
         Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct </data/belleau_lab/TeenStress/E13347949/sub-TS028/func/sub-TS028_task-rest_run-04_bold.nii.gz> for susceptibility-derived distortions.
230617-23:07:13,985 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.335s.
230617-23:07:16,370 nipype.workflow INFO:
         Setting-up fieldmap "auto_00000" (EstimatorType.ANAT) with <sub-TS028_T1w.nii.gz, sub-TS028_task-rest_run-01_bold.nii.gz, sub-TS028_task-rest_run-02_bold.nii.gz, sub-TS028_task-rest_run-03_bold.nii.gz, sub-TS028_task-rest_run-04_bold.nii.gz>
230617-23:07:16,432 nipype.workflow INFO:
         Setting-up fieldmap "auto_00001" (EstimatorType.ANAT) with <sub-TS028_T1w.nii.gz, sub-TS028_task-EMIST_run-01_bold.nii.gz, sub-TS028_task-HMIST_run-01_bold.nii.gz, sub-TS028_task-HMIST_run-02_bold.nii.gz>
230617-23:07:20,816 nipype.workflow CRITICAL:
         Cannot run fMRIPrep. Missing dependencies:
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * antsAI (Interface: AI)
        * Atropos (Interface: Atropos)
        * DenoiseImage (Interface: DenoiseImage)
        * DenoiseImage (Interface: DenoiseImage)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsApplyTransforms (Interface: FixHeaderApplyTransforms)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * antsRegistration (Interface: FixHeaderRegistration)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: FixN4BiasFieldCorrection)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * ImageMath (Interface: ImageMath)
        * MultiplyImages (Interface: MultiplyImages)
        * MultiplyImages (Interface: MultiplyImages)
        * MultiplyImages (Interface: MultiplyImages)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * N4BiasFieldCorrection (Interface: N4BiasFieldCorrection)
        * ThresholdImage (Interface: ThresholdImage)
47

Well the good news is we have a clear error message. Need to modify the PATH to include the correct ants binary path. Not at my computer, but can have a look tomorrow.

48

Just had a look. ANTs was unpacked into /opt/ants-2.4.4. Updated the Dockerfile above.

49

Worked perfectly. Thank you so much!

1 Like
50

Hello, I’m running fMRIPREP on Compute Canada, I’m not what is /PATH_TO_YOUR_TEST_OUTPUT:/work there, can you help e with that?

51

Hi @Mahsa,

This sounds like something that should be addressed in a different thread. Please review the fMRIPrep documentation here: Usage Notes — fmriprep version documentation

and notes about running containerized applications here: Executing with Singularity - NiPreps

If things still are not clear after that and your issue has not been answered elsewhere on neurostars, please open a new issue.

Best,
Steven