Hi.
I failed to run dwi2response msmt_5tt:
dwi2response:
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response:
dwi2response: Generated temporary directory: /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/dwi2response-tmp-6A3BA1/
Command: mrconvert /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/tract/MSMT_CSD_mrtrix/dti.mif /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/dwi2response-tmp-6A3BA1/dwi.mif -stride 0,0,0,1
Command: mrconvert /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/tract/MSMT_CSD_mrtrix/5tt/5tt_fsl_T12b0.mif /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/dwi2response-tmp-6A3BA1/5tt.mif
dwi2response: Changing to temporary directory (/home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/dwi2response-tmp-6A3BA1/)
Command: dwi2mask dwi.mif mask.mif
Command: 5ttcheck 5tt.mif
dwi2response: [WARNING] Command failed: 5ttcheck 5tt.mif
Command: dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif
Function: shutil.copy(vector.mif, dirs.mif)
Command: mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear
Command: mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - 0.95 -gt mask.mif -mult wm_mask.mif
dwi2response:
dwi2response: [ERROR] Command failed: mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - 0.95 -gt mask.mif -mult wm_mask.mif (msmt_5tt.py:74)
dwi2response: Output of failed command:
mrconvert: [ERROR] axis 3 provided with -coord option is out of range of input image
mrcalc: [ERROR] error converting string "-"
dwi2response: Changing back to original directory (/home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001)
dwi2response: Script failed while executing the command: mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - 0.95 -gt mask.mif -mult wm_mask.mif
dwi2response: For debugging, inspect contents of temporary directory: /home/silvia/Documenti/dottorato/EEG_data(Age-ility)/001/dwi2response-tmp-6A3BA1/
I think the problem could be the presence of only one b0 image in the dti volume.
Any idea to help me? Thanks in advance.