I am trying to run the 5ttgen fsl command to give as input to tckgen.
I have a few subjects of my dataset which fail to generate the mask at the 5ttgen step so tckgen gives empty mask error
Here is my 5ttgen command:
5ttgen fsl -nocrop -premasked $quiet -nthreads $mrtrixthreads $force -nocleanup $imputedimg 5tt.nii.gz
The imputedimg is an imputed T1w from my patient cohort.
For the unsuccessful cases, the orientation information was as follows:
Orientation : PSR
Primary Slice Direction: sagittal
However, I have a few other subjects with the same orientation information for which the 5ttgen ran successfully.
Could you please advise?