# Dhollander/msmt\_csd - corrupted FOD images

**URL:** <https://community.mrtrix.org/t/dhollander-msmt-csd-corrupted-fod-images/6450>\
**Category:** Uncategorized\
**Tags:** dwi2fod, dwi2response\
**Created:** [March 1, 2023, 2:34pm UTC](https://community.mrtrix.org/t/dhollander-msmt-csd-corrupted-fod-images/6450 "2023-03-01T14:34:18Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ozgezer](https://community.mrtrix.org/user_avatar/community.mrtrix.org/ozgezer/32/4008_2.png) [@ozgezer](https://community.mrtrix.org/u/ozgezer)\
**Post date:** [March 1, 2023, 2:34pm UTC](https://community.mrtrix.org/t/dhollander-msmt-csd-corrupted-fod-images/6450/1 "2023-03-01T14:34:18Z")

</div>

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:

```auto
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!!

 ![fod_normal](https://community.mrtrix.org/uploads/default/original/2X/6/666c6940f24769724c8231bd3eac362264e8d3af.png)  
 ![fod_weird](https://community.mrtrix.org/uploads/default/original/2X/a/a246dfba5e59a49cfbfcfb4cc28b1f5a570ab0b3.png)

---

<div class="post-metadata">

**Author:** ![bjeurissen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/bjeurissen/32/28_2.png) [@bjeurissen](https://community.mrtrix.org/u/bjeurissen)\
**Post date:** [March 2, 2023, 7:38am UTC](https://community.mrtrix.org/t/dhollander-msmt-csd-corrupted-fod-images/6450/2 "2023-03-02T07:38:07Z")

</div>

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

1. Inspect the input DWI data. Any obvious differences between the good and bad dataset?

2. 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

---

<div class="post-metadata">

**Author:** ![ozgezer](https://community.mrtrix.org/user_avatar/community.mrtrix.org/ozgezer/32/4008_2.png) [@ozgezer](https://community.mrtrix.org/u/ozgezer)\
**Post date:** [March 2, 2023, 8:54am UTC](https://community.mrtrix.org/t/dhollander-msmt-csd-corrupted-fod-images/6450/3 "2023-03-02T08:54:39Z")

</div>

Thanks a lot for your reply Ben.

1. I couldn’t detect any obvious differences between those two datasets.
2. 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.

 ![baddata](https://community.mrtrix.org/uploads/default/original/2X/0/0e8671ce2414555a12bf41ee2f23796e14cc1dc8.png)  
 ![gooddata](https://community.mrtrix.org/uploads/default/original/2X/3/3cc72102386a6480269b205e999146525cbfa059.png)

![shview](https://community.mrtrix.org/uploads/default/original/2X/9/9076bb107f636381b26230c362fbefdfc7e9062e.png)