# What the result of two shells (one 0, one 1500) using msmt\_csd should look like? **URL:** \ **Category:** Uncategorized\ **Tags:** tractography\ **Created:** [March 21, 2025, 5:51pm UTC](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291 "2025-03-21T17:51:01Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Yufeng\_He](https://community.mrtrix.org/user_avatar/community.mrtrix.org/yufeng_he/32/5003_2.png) [@Yufeng\_He](https://community.mrtrix.org/u/Yufeng_He)\ **Post date:** [March 21, 2025, 5:51pm UTC](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291/1 "2025-03-21T17:51:01Z")
Dear Community, I’m generating FOD for my two shells(0,1500), 60 directions data, using the **MSMT-CSD** method.I want to check my generated fod map to make sure everything is ok. But I suddenly realised that there are very few tutorials on what the results of two shell analysis using MSMT-CSD should look like.The tutorial on **[Andy’s book](https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html) and [BATMAN](https://osf.io/fkyht/)**, which used data from larger than two shells, obtained results similar to Figure 1.But I find this very different from the results I generated. Anyway I want to make sure that my results are normal. If it is wrong, is there something wrong there? I hope to get replies from all of you. Thanks. This is the code I used to generate the WM,GM, CSF response function, and FOD. ```auto # use dhollander dwi2response dhollander preproc_unbiased.mif \ wm_response.txt gm_response.txt csf_response.txt -voxels voxels.mif # Upsample mrgrid preproc_unbiased.mif regrid -vox 1.25 preproc_unbiased_upsample.mif # FOD MSMT,only WM and CSF dwi2fod -force msmt_csd preproc_unbiased_upsample.mif \ -mask mask_upsample.mif \ wm_response.txt wmfod.mif \ csf_response.txt csffod.mif # check result mrconvert -coord 3 0 wmfod.mif - | mrcat csffod.mif - 2_tiusses_combin.mif mrview 2_tiusses_combin.mif -odf.load_sh wmfod.mif ``` This is the result picture of BATMAN. ![image](https://community.mrtrix.org/uploads/default/original/2X/4/4fb99d8c8645072c52c5bc8c97687aad88eed88c.jpeg) And,this is the picture of my result. I would like to know if this result is normal? ![image](https://community.mrtrix.org/uploads/default/original/2X/0/061ae54b7bf91cfa6be3c819b5064bab25476572.jpeg) On top of that, I’m confused about the resulting wm\_fod.mif and the cdf\_fod.mif produced after dwi2fod is about? I checked both results using mrinfo and found that they have different volume counts. （The volume number of wm\_fod is less than the volume number of my raw data，10b0 + 60 1500). ![image](https://community.mrtrix.org/uploads/default/original/2X/7/7c74742c1b7a6a8638e846a8f7f0f3b05e22c272.png) ![image](https://community.mrtrix.org/uploads/default/original/2X/a/a84a18558b668f3b0043c249d709ead1a230fd53.png) Also I noticed that [ss3t\_csd\_beta1](https://3tissue.github.io/doc/ss3t-csd.html) is available on MRtrix3Tissue for single shell data. I wonder which method is right for my data?🤔 Anyway hope to get everyone’s input and if anyone has any insight please let me know. Thanks. Yufeng ---
**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 21, 2025, 10:24pm UTC](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291/2 "2025-03-21T22:24:48Z")
I don’t see anything wrong. > [@Yufeng\_He](#): > > ```auto > mrconvert -coord 3 0 wmfod.mif - | mrcat csffod.mif - 2_tiusses_combin.mif > > ``` Maybe better to convert them as: ```auto mrconvert -coord 3 0 wmfod.mif - | mrcat csffod.mif $(mrcalc csffod.mif 0 -multiply -) - vf.mif ``` This adds an extra color channel for the missing GM (and sets it to zero), such that you get the same RGB style image (albeit without GM compartment (green)). > [@Yufeng\_He](#): > > On top of that, I’m confused about the resulting wm\_fod.mif and the cdf\_fod.mif produced after dwi2fod is about? I checked both results using mrinfo and found that they have different volume counts. （The volume number of wm\_fod is less than the volume number of my raw data，10b0 + 60 1500). Functions of the sphere (such as the FOD) are represented using spherical harmonics coefficients (see [Spherical Harmonics — MRtrix3 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/concepts/spherical_harmonics.html) for details). Isotropic compartments (such as CSF and GM) only require 1 coefficient, as they don’t have to model any angular dependency (hence the one in the final dimension of csffod) Anisotropic compartments (such as WM) typically require 45 coefficients (corresponding to SH order 8), hence the 45 in the fina dimension of wmfod. . ---
**Author:** ![Yufeng\_He](https://community.mrtrix.org/user_avatar/community.mrtrix.org/yufeng_he/32/5003_2.png) [@Yufeng\_He](https://community.mrtrix.org/u/Yufeng_He)\ **Post date:** [March 22, 2025, 11:27am UTC](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291/3 "2025-03-22T11:27:20Z")
> [@bjeurissen](#): > > I don’t see anything wrong. Thanks for your reply, that’s great. I’m happy I’m doing the right thing. > [@bjeurissen](#): > > Maybe better to convert them as: > > ```auto > mrconvert -coord 3 0 wmfod.mif - | mrcat csffod.mif $(mrcalc csffod.mif 0 -multiply -) - vf.mif > > ``` > > This adds an extra color channel for the missing GM (and sets it to zero), such that you get the same RGB style image (albeit without GM compartment (green)). The results look better.Like, ![image](https://community.mrtrix.org/uploads/default/original/2X/4/48b406b4f2787bd613bb826e9bc1566da4b33f41.jpeg) > [@bjeurissen](#): > > Functions of the sphere (such as the FOD) are represented using spherical harmonics coefficients (see [Spherical Harmonics — MRtrix3 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/concepts/spherical_harmonics.html) for details). > > Isotropic compartments (such as CSF and GM) only require 1 coefficient, as they don’t have to model any angular dependency (hence the one in the final dimension of csffod) > Anisotropic compartments (such as WM) typically require 45 coefficients (corresponding to SH order 8), hence the 45 in the fina dimension of wmfod. Thanks for your information, I will carefully check the document about the Spherical Harmonics.