FSL's feat working through GUI while failing on the command line

Software Support
1

Hi!
I’m running a first level analysis on fMRI data using feat, including the preprocessing steps.
I’m generating the .fsf file based on a template, then calling feat generated.fsf.
When I do it this way the analysis fails during registration, apparantly because it’s looking for some example_func file or some such - but really the errors and stack are quite cryptic.

The thing is that when I open the GUI and load the exact same .fsf file and hit ‘Go’ - the analysis completes without problems.

I’d appreciate any help - thanks!

Version:

FSL 6.0.6

Environment (Docker, Singularity, custom installation):

Ubuntu 20

Relevant log outputs (up to 20 lines):

Registration

/bin/mkdir -p /media/user/Data/fmri-data/analysis-output/101/functional/sub101_auditoryLoc_1.feat/reg

Could not find a supported file with prefix "/media/user/Data/fmri-data/analysis-output/101/functional/sub101_auditoryLoc_1.feat/example_func"

/home/user/fsl/bin/fslmaths /media/user/Data/fmri-data/analysis-output/101/anatomy/101anatomy_brain highres


/home/user/fsl/bin/fslmaths /media/user/Data/fmri-data/analysis-output/101/anatomy/101anatomy  highres_head

Checking for /media/user/Data/fmri-data/analysis-output/101/anatomy/101anatomy_brain2MNI152_T1_2mm_brain_warp and /media/user/Data/fmri-data/analysis-output/101/anatomy/101anatomy_brain2MNI152_T1_2mm_brain.mat

/home/user/fsl/bin/fslmaths /home/user/fsl/data/standard/MNI152_T1_2mm_brain standard


/home/user/fsl/bin/fslmaths /home/user/fsl/data/standard/MNI152_T1_2mm standard_head


/home/user/fsl/bin/fslmaths /home/user/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil standard_mask

did not find file: example_func2highres.mat. Generating transform.

/home/user/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
Image Exception : #63 :: No image files match: example_func
Image Exception : #22 :: Failed to read volume example_func
Error : No image files match: example_func
Failed to read volume example_func
Error : No image files match: example_func
Image Exception : #63 :: No image files match: example_func
Image Exception : #22 :: Failed to read volume example_func
Error : No image files match: example_func
Failed to read volume example_func
Error : No image files match: example_func
Could not open matrix file example_func2highres.mat
Image Exception : #63 :: No image files match: example_func
Image Exception : #22 :: Failed to read volume example_func
Error : No image files match: example_func
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume example_func
Error : No image files match: example_func
/home/user/fsl/bin/epi_reg: line 390: 623496 Aborted                 (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
Running FAST segmentation FLIRT pre-alignment Running BBR
2

Hi, I recently had a similar experience. In my case, there was an error in the design.fsf file that was being overwritten when I opened it in the FSL GUI. Specifically, a typo in the template and script that generated the design.fsf file made it so that the number of volumes for my functional data was set to 0; but, when I opened the file in FSL, it read the input data and automatically corrected the number of volumes. As a result, the .fsf file would not run when I called feat design.fsf in the command line, but it did work when I clicked “Go” in the FSL GUI. After fixing the number of volumes in the .fsf file, it works from the command line again.

I would recommend opening the .fsf file in a text editor and in the FSL GUI side-by-side to confirm that all the settings are the same. If your issue is like mine, there may be an incorrect setting in your file that is being corrected/overwritten when you open the file in the GUI.

Best,
Jimmy