Congratulations to the developers on an outstanding release and thank you for all the hard work.
I am attempting to follow the structural connectome tutorial but substituting my own data. My data only has a single b=0 image at the beginning. I am new to this field so I may have missed something.
This problem appears related to Error in dwi2response with msmt_5tt
“… the command responsible for averaging the b=0 volumes fails because a single volume comes out from the previous command as a 3D image, so there is no 4th axis to average over.”
On the diffusion image processing sub heading step 2 and step 3 fail.
For step 2:
dwiextract DWI.mif - -bzero | mrmath - mean meanb0.mif -axis 3
dwiextract: [100%] extracting volumes
mrmath: [ERROR] Cannot perform operation along axis 3; image only has 3 axes
For step 3:
dwi2response msmt_5tt DWI.mif 5TT.mif RF_GM.txt RF_WM.txt RF_CSF.txt -voxels RF_voxels.mif
dwi2response:
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwi2response:
dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-DTXN5P/
Command: mrconvert 5TT.mif /tmp/dwi2response-tmp-DTXN5P/5tt.mif -quiet
Command: mrconvert DWI.mif /tmp/dwi2response-tmp-DTXN5P/dwi.mif -stride 0,0,0,1 -quiet
dwi2response: Changing to temporary directory (/tmp/dwi2response-tmp-DTXN5P/)
Command: dwi2mask dwi.mif mask.mif -quiet
dwi2response: [WARNING] Less than three b-value shells; response functions will not be applicable in MSMT CSD algorithm
Command: dwi2tensor dwi.mif - -mask mask.mif -quiet | tensor2metric - -fa fa.mif -vector vector.mif -quiet
Command: mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt fa.mif 0.2 -lt -mult mask.mif -mult gm_mask.mif -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt mask.mif -mult wm_mask.mif -quiet
Command: mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 -quiet | mrcalc - 0.95 -gt fa.mif 0.2 -lt -mult mask.mif -mult csf_mask.mif -quiet
dwi2response: Calling dwi2response recursively to select WM single-fibre voxels using ‘tournier’ algorithm
Command: dwi2response -quiet tournier dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif
Command: dwiextract dwi.mif -shell 0.0 dwi_b0.mif -quiet
Command: amp2sh dwi_b0.mif - -quiet | sh2response - wm_sf_mask.mif dirs.mif wm_response_b0.txt -quiet
amp2sh: [ERROR] dwi image should contain 4 dimensions
sh2response: [ERROR] no filename supplied to standard input (broken pipe?)
sh2response: [ERROR] error opening image "-"
dwi2response: [ERROR] Command failed: amp2sh dwi_b0.mif - -quiet | sh2response - wm_sf_mask.mif dirs.mif wm_response_b0.txt -quiet
dwi2response: Changing back to original directory (/home/tom/ACT/FAST)
dwi2response: Deleting temporary directory /tmp/dwi2response-tmp-DTXN5P/