Open ariveradompenciel opened 4 years ago
if you have fsl installed, could you give the output of fslhd <name of anatomical file>
or with fmriprep singularity image you can execute something like:
singularity exec -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL224/path/to/anatomical/file
and then do the same for a participant that has successfully completed in the PIL project (are there any?)
I want to know if this participant's anatomical image is a different size than another participant's anatomical image.
do not have fsl. I was also unsure of which anat file to use, so tried three different files (two of which I saw in error output) for singularity. all three failed (as well as for a successfully run PIL sub):
singularity exec -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL224/anat_preproc_wf/surface_recon_wf/autorecon1
/mnt/Projects/CREST/sub-PIL224/anat_preproc_wf/surface_recon_wf/autorecon1 failed
singularity exec -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL224/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-PIL224_T1w_ras.nii.gz
/mnt/Projects/CREST/sub-PIL224/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-PIL224_T1w_ras.nii.gz failed
singularity exec -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL224/anat/sub-PIL224_desc-preproc_T1w.nii.gz
/mnt/Projects/CREST/sub-PIL224/anat/sub-PIL224_desc-preproc_T1w.nii.gz failed
You were close, I was trying to suggest the original t1w file
Here's what I wanted:
singularity exec -B /Shared/vosslabhpc:/mnt /Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL224/anat/sub-PIL224_T1w.nii.gz
output:
/mnt/Projects/CREST/sub-PIL224/anat/sub-PIL224_T1w.nii.gz int16 [256, 240, 256] 1.00x1.40x1.00 sform
Could you do the same for a successful run?
Oh sorry, thanks for clarifying! Here is the code and output for two successful runs:
singularity exec -B /Shared/vosslabhpc:/mnt /Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL220/anat/sub-PIL220_T1w.nii.gz
/mnt/Projects/CREST/sub-PIL220/anat/sub-PIL220_T1w.nii.gz int16 [256, 240, 256] 1.00x1.00x1.00
singularity exec -B /Shared/vosslabhpc:/mnt /Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg nib-ls /mnt/Projects/CREST/sub-PIL227/anat/sub-PIL227_T1w.nii.gz
/mnt/Projects/CREST/sub-PIL227/anat/sub-PIL227_T1w.nii.gz int16 [256, 240, 256] 1.00x1.00x1.00
Seems sub-PIL224's anatomical image is of a different size…
it's weird that sub-PIL224 voxel sizes are not isotropic (not the same number for all dimensions) 1.00x1.40x1.00
, while the other participants are isotropic: 1.00x1.00x1.00
.
I would look at the image in a viewer and see if the image looks stretched/compressed relative to other participants, or somehow check if the dimensions should be 1.00x.1.40x1.00
(do you have access to the original dicom images?).
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