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ciftify_recon_all error
runngin ciftify_recon_all in a docker container leads to:
Traceback (most recent call last):
File "/home/code/ciftify/ciftify/bin/ciftify_recon_all", line 1570, in
Registration Sphere /ciftify/sub-10/MNINonLinear/Native/sub-10.L.sphere.MSMSulc.native.surf.gii not found
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2021-08-12 14:03:23.607210 : Starting cifti_recon_all
Creating tempdir:/tmp/tmp5p81v25i on host:19d788b2c090 Arguments: freesurfer SUBJECTS_DIR: /data/derivatives/freesurfer CIFTIFY_WORKDIR directory: /ciftify Subject: sub-10 MSM config file: /home/code/ciftify/ciftify/data/hcp_config/MSMSulcStrainFinalconf
---### Environment Settings ###--- Username: root System Info: OS: Linux Hostname: 19d788b2c090 Release: 5.4.0-80-generic Version: #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 Machine: x86_64 ciftify: Path: /home/code/ciftify/ciftify/bin Commit: ce1876b22747ef76b797de5056ec38cab8fc5e66 Author: Erin W Dickie [email protected] Last commit for ciftify_recon_all: Commit: a2f653b92df346cc615347d61de0a22a5cef8ddc Date: Mon Jul 24 17:34:42 2017 -0400 wb_command: Path: /usr/bin/wb_command Version: 1.3.2 Commit Date: unknown Operating System: Linux freesurfer: Path: /opt/freesurfer/bin Build Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a FSL: Path: /usr/share/fsl/5.0 Version: 5.0.9 ---### End of Environment Settings ###---
recon_all was run Wed Mar 10 08:25:41 CET 2021 with settings: Build Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Version parsed as: v6.0.0 CMD args: -all -subjid sub-100010 -parallel -openmp 8 -cw256 -no-isrunning
2021-08-12 14:03:23.852403 : Converting T1wImage and Segmentations from freesurfer
Running: mri_convert /data/derivatives/freesurfer/sub-10/mri/T1.mgz /ciftify/sub-10/T1w/T1w.nii.gz mri_convert.bin /data/derivatives/freesurfer/sub-10/mri/T1.mgz /ciftify/sub-10/T1w/T1w.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/derivatives/freesurfer/sub-10/mri/T1.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-1.86265e-09, 1, 0) writing to /ciftify/sub-10/T1w/T1w.nii.gz...
Running: fslreorient2std /ciftify/sub-10/T1w/T1w.nii.gz /ciftify/sub-10/T1w/T1w.nii.gz Running: mri_convert -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/wmparc.mgz /ciftify/sub-10/T1w/wmparc.nii.gz mri_convert.bin -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/wmparc.mgz /ciftify/sub-10/T1w/wmparc.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/derivatives/freesurfer/sub-10/mri/wmparc.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-1.86265e-09, 1, 0) reading template info from volume /ciftify/sub-10/T1w/T1w.nii.gz... changing data type from int to float (noscale = 0)... Reslicing using nearest writing to /ciftify/sub-10/T1w/wmparc.nii.gz...
Running: wb_command -logging SEVERE -volume-label-import /ciftify/sub-10/T1w/wmparc.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/T1w/wmparc.nii.gz -drop-unused-labels Running: mri_convert -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/aparc.a2009s+aseg.mgz /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz mri_convert.bin -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/aparc.a2009s+aseg.mgz /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/derivatives/freesurfer/sub-10/mri/aparc.a2009s+aseg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-1.86265e-09, 1, 0) reading template info from volume /ciftify/sub-10/T1w/T1w.nii.gz... changing data type from int to float (noscale = 0)... Reslicing using nearest writing to /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz...
Running: wb_command -logging SEVERE -volume-label-import /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz -drop-unused-labels Running: mri_convert -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/aparc+aseg.mgz /ciftify/sub-10/T1w/aparc+aseg.nii.gz mri_convert.bin -rt nearest -rl /ciftify/sub-10/T1w/T1w.nii.gz /data/derivatives/freesurfer/sub-10/mri/aparc+aseg.mgz /ciftify/sub-10/T1w/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/derivatives/freesurfer/sub-10/mri/aparc+aseg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 0) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-1.86265e-09, 1, 0) reading template info from volume /ciftify/sub-10/T1w/T1w.nii.gz... changing data type from int to float (noscale = 0)... Reslicing using nearest writing to /ciftify/sub-10/T1w/aparc+aseg.nii.gz...
Running: wb_command -logging SEVERE -volume-label-import /ciftify/sub-10/T1w/aparc+aseg.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/T1w/aparc+aseg.nii.gz -drop-unused-labels
2021-08-12 14:03:38.820609 : Creating brainmask from freesurfer wmparc segmentation
Running: fslmaths /ciftify/sub-10/T1w/wmparc.nii.gz -bin -dilD -dilD -dilD -ero -ero /ciftify/sub-10/T1w/brainmask_fs.nii.gz Running: wb_command -volume-fill-holes /ciftify/sub-10/T1w/brainmask_fs.nii.gz /ciftify/sub-10/T1w/brainmask_fs.nii.gz Running: fslmaths /ciftify/sub-10/T1w/brainmask_fs.nii.gz -bin /ciftify/sub-10/T1w/brainmask_fs.nii.gz Running: fslmaths /ciftify/sub-10/T1w/T1w.nii.gz -mul /ciftify/sub-10/T1w/brainmask_fs.nii.gz /ciftify/sub-10/T1w/T1w_brain.nii.gz
2021-08-12 14:05:45.184760 : Registering T1wImage to MNI template using FSL FNIRT
Running: flirt -interp spline -dof 12 -in /ciftify/sub-10/T1w/T1w_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz -omat /ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /tmp/tmp5p81v25i/T1w2StandardLinearImage.nii.gz Running: fnirt --in=/tmp/tmp5p81v25i/T1w2StandardLinearImage.nii.gz --ref=/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz --refmask=/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz --fout=/ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --logout=/ciftify/sub-10/MNINonLinear/xfms/NonlinearReg_fromlinear.log --config=/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_2mm.cnf Running: invwarp -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz -o /ciftify/sub-10/MNINonLinear/xfms/Standard2T1w_warp_noaffine.nii.gz -r /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz Running: applywarp --rel --interp=trilinear -i /ciftify/sub-10/T1w/T1w.nii.gz -r /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /ciftify/sub-10/MNINonLinear/T1w.nii.gz
2021-08-12 14:11:01.248414 : Applying MNI transform to label files
Running: applywarp --rel --interp=nn -i /ciftify/sub-10/T1w/wmparc.nii.gz -r /ciftify/sub-10/MNINonLinear/T1w.nii.gz -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /ciftify/sub-10/MNINonLinear/wmparc.nii.gz Running: wb_command -volume-label-import -logging SEVERE /ciftify/sub-10/MNINonLinear/wmparc.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/MNINonLinear/wmparc.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /ciftify/sub-10/T1w/aparc.a2009s+aseg.nii.gz -r /ciftify/sub-10/MNINonLinear/T1w.nii.gz -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /ciftify/sub-10/MNINonLinear/aparc.a2009s+aseg.nii.gz Running: wb_command -volume-label-import -logging SEVERE /ciftify/sub-10/MNINonLinear/aparc.a2009s+aseg.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/MNINonLinear/aparc.a2009s+aseg.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /ciftify/sub-10/T1w/aparc+aseg.nii.gz -r /ciftify/sub-10/MNINonLinear/T1w.nii.gz -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /ciftify/sub-10/MNINonLinear/aparc+aseg.nii.gz Running: wb_command -volume-label-import -logging SEVERE /ciftify/sub-10/MNINonLinear/aparc+aseg.nii.gz /home/code/ciftify/ciftify/data/hcp_config/FreeSurferAllLut.txt /ciftify/sub-10/MNINonLinear/aparc+aseg.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /ciftify/sub-10/T1w/brainmask_fs.nii.gz -r /ciftify/sub-10/MNINonLinear/T1w.nii.gz -w /ciftify/sub-10/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/ciftify/sub-10/MNINonLinear/xfms/T1w2StandardLinear.mat -o /ciftify/sub-10/MNINonLinear/brainmask_fs.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-10/T1w/Native/sub-10.native.wb.spec INVALID /ciftify/sub-10/T1w/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-10/MNINonLinear/Native/sub-10.native.wb.spec INVALID /ciftify/sub-10/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-10/MNINonLinear/sub-10.164k_fs_LR.wb.spec INVALID /ciftify/sub-10/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-10/MNINonLinear/fsaverage_LR32k/sub-10.32k_fs_LR.wb.spec INVALID /ciftify/sub-10/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-10/T1w/fsaverage_LR32k/sub-10.32k_fs_LR.wb.spec INVALID /ciftify/sub-10/T1w/T1w.nii.gz Running: mkdir -p /ciftify/zz_templates Running: cp /home/code/ciftify/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz /ciftify/zz_templates/Atlas_ROIs.2.nii.gz
Here it stops
From the Error message - it's makes me wonder if you have run out the tmp storage space during the pipeline? (so it's stopped copying templates into temp)
How much temp space do you have available for this pipeline?
do you mean I should give the docker more space? I think standard is 10GB. So increase it to 20GB?
I think the problem is that this file: /home/code/ciftify/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz does not exist for copying. ciftify is a path specified in the docker container I created.
How does the ciftify code come up with /home/code.... ?
weird - so if you built the container yourself - a clone of the ciftify github repo needs to be in the ciftify path (in this case - /home/code/ciftify) the repo contains a data folder with some template files (including the 91282_Greyordinates/Atlas_ROIs.2.nii.gz).
Yes, because this is used to build the docker container:
setting up an install of ciftify (manual version) inside the container
ADD https://api.github.com/repos/edickie/ciftify/git/refs/heads/master version.json RUN mkdir /home/code && git clone -b master https://github.com/edickie/ciftify.git /home/code/ciftify
ENV PATH=/home/code/ciftify/ciftify/bin:${PATH}
PYTHONPATH=/home/code/ciftify:${PYTHONPATH}
CIFTIFY_TEMPLATES=/home/code/ciftify/ciftify/data
WORKDIR /HOME/Pipeline/
ENTRYPOINT []
but still it works until here: Running: wb_command -add-to-spec-file /ciftify/sub-68/MNINonLinear/fsaverage_LR32k/sub-68.32k_fs_LR.wb.spec INVALID /ciftify/sub-68/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-68/T1w/fsaverage_LR32k/sub-68.32k_fs_LR.wb.spec INVALID /ciftify/sub-68/T1w/T1w.nii.gz Running: mkdir -p /ciftify/zz_templates Running: cp /home/code/ciftify/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz /ciftify/zz_templates/Atlas_ROIs.2.nii.gz
so it copies the Atlas_ROIs.2. into the zz_template folder.
In the terminal it says then:
Traceback (most recent call last):
File "/home/code/ciftify/ciftify/bin/ciftify_recon_all", line 1570, in
so the Atlas_ROIs.2.nii.gz is not linked into the subjects ROI folder.
code from ciftify_recon_all line 533 is the last line inhere:
def link_to_template_file(settings, subject_file, global_file, via_file): ''' The original hcp pipelines would copy atlas files into each subject's directory, which had the benefit of making the atlas files easier to find and copy across systems but created many redundant files. This function instead will copy the atlas files into a templates directory in the CIFTIFY_WORKDIR Folder and then link from each subject's individual directory to this file ''' if settings.no_symlinks: run(['cp', global_file, subject_file], dryrun=DRYRUN) else: ## copy from ciftify template to the HCP_DATA if via_file does not exist via_folder = os.path.join(settings.work_dir, 'zz_templates') via_path = os.path.join(via_folder, via_file) if not os.path.isfile(via_path): if not os.path.exists(via_folder): run(['mkdir','-p',via_folder], dryrun=DRYRUN) run(['cp', global_file, via_path], dryrun=DRYRUN) ## link the subject_file to via_file if not DRYRUN: os.symlink(os.path.relpath(via_path, os.path.dirname(subject_file)), subject_file)
Do you have any idea?