Summary of what happened:
Hello,
I have used MRIQC (0.15.1) in the past with raw T1w images (1.5T, 3T, and synthesized) but now I’m running into errors when I try to run pre-processed images. All of my images are in the BIDS format. I am trying to compare the quality of images pre-processed through different toolboxes (CAT12, MALP-EM, volBrain). The volBrain output is run through MRIQC with no problems, but the CAT12 and MALP-EM outputs crash during the skullstripping step for seemingly different reasons. I have tried to realign the MALP-EM images, I have run the --deoblique specification in the command, and I have run them on both a participant and group level but so far nothing has worked.
Any help would be very much appreciated!
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
MRIQC 0.15.1
CAT12 v?
MALP-EM v?
volBrain v?
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Here is the CAT12 output error:
RuntimeError: Command:
3dSkullStrip -input /mnt/d/outputfolder/BIDS_3T_CAT12/derivatives/mriqc/sub-003/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file–data–sub-018..anat..sub-018_T1w.nii.gz/skullstrip/sub-018_t1w_conformed_corrected.nii.gz -prefix sub-018_t1w_confirmed_corrected_skullstrip.nii.gz
Standard output:
Standard error:
Oo Warning 3dSkullStrip (SUMA_3dSkullStrip.c:1565):
Input dataset has a very low value range.
If stripping fails, repeat with option -fac 1000
– Error SUMA_LoadPrepInVol (SUMA_BrainWrap.c:77):
98 percentile is 0!
What kind of dataset is this?
– Error 3dSkullStrip (SUMA_3dSkullStrip.c:2027);
Failed to load/prep volume
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /root/.afni.crashlog
Return code: 1
And here is the MALP-EM output error:
RuntimeError: Command:
3dSkullStrip -input /mnt/d/outputfolder/BIDS_3T_MALPEM/derivatives/mriqc/sub-003/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file–data–sub-018..anat..sub-018_T1w.nii.gz/skullstrip/sub-018_t1w_conformed_corrected.nii.gz -prefix sub-018_t1w_confirmed_corrected_skullstrip.nii.gz
Standard output:
e[7m+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as /mnt/d/outputfolder/BIDS_3T_MALPEM/derivatives/mriqc/sub-003/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file–data–sub-018..anat..sub-018_T1w.nii.gz/skullstrip/sub-018_t1w_conformed_corrected.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique
Fatal Signal 11 (SIGSEGV) received
SUMA_SurfGrideIntersect
SUMA_FindVoxelsInSurface
3dSkullStrip
Bottom of Debug Stack
**AFNI version = AFNI_17.3.03 Compile date = Nov 9 2017
**[[Precompiled binary linux_ubuntu_16_64: Nov 9 2017]]
**Program Death**
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /root/.afni.crashlog
Return code: 1