‘dwi2response dhollander’ script outputs error

1

Hi MRtrix3 experts,

I want to evaluate the performance of ‘dwi2response dhollander’ script on single-shell data with 2 unique b-value(s): 0 and 1000.
For this purpose, I’ve run the following command:

dwi2response dhollander dwi_denoised_eddy_unbiased.mif response_wm.txt response_gm.txt response_csf.txt

However, I got the following error inspecting the dwi2response-tmp-LNTX33 folder:

mrconvert voxels.mif /Volumes/WD_Elements/BROAD/DTI/Fixel_Based_Analysis/subjects/sub-52/dwi2response-tmp-LNTX33/voxels_sfwm.mif -copy_properties /Volumes/WD_Elements/BROAD/DTI/Fixel_Based_Analysis/subjects/sub-52/dwi2response-tmp-LNTX33/dwi.mif -append_property command_history "/Users/davidemomi/mrtrix3/bin/dwi2response \"tournier\" \"dwi.mif\" \"_respsfwmss.txt\" \"-sf_voxels\" \"1825\" \"-iter_voxels\" \"18250\" \"-mask\" \"refined_wm.mif\" \"-voxels\" \"voxels_sfwm.mif\" \"-tempdir\" \"/Volumes/WD_Elements/BROAD/DTI/Fixel_Based_Analysis/subjects/sub-52/dwi2response-tmp-LNTX33/\"  (version=3.0_RC3-206-g80288328)"

mrconvert: [ERROR] unknown option "-copy_properties"

Do you have any suggestions?

Thanks

3

Hi @ThijsDhollander,

thanks for your follow up, it was really helpful. I just update the mrtrix3 and I was finally able to run the command

dwi2response dhollander dwi_denoised_eddy_unbiased.mif response_wm.txt response_gm.txt response_csf.txt

However the response_wm looks weird to me (see image below)

49

it supposes to be different right?

Moreover, even though I’ve updated mrtrix3 I wasn’t able to find the ss3t_csd_beta1 command. So I’ve basically downloaded the source code from this link:

and then I’ve just copied and pasted the ss3t_csd_beta1 into mrtrix/bin directory.

Do you think this is the correct procedure?

ps: I’ve preprocessed my data without Gibbs ringing removal. Do you think might be a problem? Should I preprocess the data from scratch?

Thanks

Davide