Dwi2response msmt_5tt [ERROR]: axis 3 provided with -coord option is out of range of input image


#1

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.


#2

Hi Silvia,

I think the underlying issue is indicated earlier:

Command: 5ttcheck 5tt.mif
dwi2response: [WARNING] Command failed: 5ttcheck 5tt.mif

My suspicion is that your image “5tt.mif” is actually a 3D image, not 4D; hence the later error message:
mrconvert: [ERROR] axis 3 provided with -coord option is out of range of input image

Details on the 5TT format are here. You can also try calling the 5ttcheck command directly on your image to see what it says.

Rob