Dhollander/msmt_csd - corrupted FOD images

ozgezer · March 1, 2023, 2:34pm

Hi all,

I have been running dwi2response dhollander and dwi2fod msmt_csd to generate FOD maps for each subject in my data. However, when I check each individual’s voxels.mif/vf.mif data, some of data have corrupted/abnormal FOD maps. I couldn’t find what is common among those corrupted images, and I am not sure what kind of parameters I should check.

These are the codes I ran:

dwi2response dhollander ${dir}/${subname}/${subname}_unbiased.mif -fslgrad ${dir}/${subname}/${subname}_merged_dwi_gibbsCorrSubVoxShift_TED_synthB0.bvec ${dir}/${subname}/${subname}_merged_dwi_gibbsCorrSubVoxShift_TED_synthB0.bval ${dir}/${subname}/${subname}_response_wm.txt ${dir}/${subname}/${subname}_response_gm.txt ${dir}/${subname}/${subname}_response_csf.txt -voxels ${dir}/${subname}/${subname}_voxels.mif
dwi2fod msmt_csd ${dir}/${subname}/${subname}_unbiased.mif -fslgrad ${dir}/${subname}/${subname}_merged_dwi_gibbsCorrSubVoxShift_TED_synthB0.bvec ${dir}/${subname}/${subname}_merged_dwi_gibbsCorrSubVoxShift_TED_synthB0.bval ${dir}/${subname}/${subname}_response_wm.txt ${dir}/${subname}/wmfod.mif ${dir}/${subname}/${subname}_response_gm.txt ${dir}/${subname}/gmfod.mif  ${dir}/${subname}/${subname}_response_csf.txt ${dir}/${subname}/csffod.mif -mask ${dir}/${subname}/${subname}_masked.mif 
 
mrconvert -coord 3 0 ${dir}/${subname}/wmfod.mif - | mrcat ${dir}/${subname}/csffod.mif ${dir}/${subname}/gmfod.mif - ${dir}/${subname}/vf.mif

I would appreciate it a lot if you suggest me anything that might be causing this and how to resolve it.

I attached the images of a normal, and corrupted FOD maps.

Many thanks in advance!!

bjeurissen · March 2, 2023, 7:38am

Rather than looking at / reporting the final result, please inspect/report the outcome of the individual steps, e.g.

Inspect the input DWI data. Any obvious differences between the good and bad dataset?
Inspect the output of dwi2response:

did the command output any warnings?
overlay voxels.mif on an anatomical scan to check if the exemplar voxels for each tissue type are in the right places
open the response functions (txt files) with a text editor and inspect the first column: for each tissue type, do you observe a similar b-value dependent decay in the corrupted vs good case?
inspect the response functions (txt files) with shview

ozgezer · March 2, 2023, 8:54am

Thanks a lot for your reply Ben.

I couldn’t detect any obvious differences between those two datasets.
There were not any warnings, however, csf does not seem right in the right place for bad data (as below). I am quite new at mrtrix, but I couldn’t see any obvious differences in the response function (txt files). On the other hand, csf is clearly getting less smaller in the bad data comapred to good data. I added the images for these as well, the elft one is good, and the right one is the bad data.

shview