[RESOLVED] Import MRTrix data to dwi_parcellate?

1

Hi all

Would it be possible to import MRtrix whole head tractographies to be parcellated using dwi_parcellate?

Thanks in advance,
Karin

2

Hi,

Could you tell a bit more about your MRtrix data. What format is it in, dconn.nii.gz?

Best, Jure

3

Hi

MRTrix uses .mif file format (but can be converted to .nii)

Best
Karin

4

Hi,

QuNex dwi_parcellate is coded so it seamlessy integrates with hcp_diffusion and dwi_legacy_gpu for legacy data acquisition style. For your use case it would be better to use wb_command directly. I am not familiar with MRtrix data, however this might work:

# 1. convert MRtrix .mif to .nii
# Unfortunately, you are on your own here as I never worked with MRtrix before

# 2. Use wb_command to parcellate the data
# first by ROW
wb_command -cifti-parcellate "<path_to_input_nii>" "<path _to_parcellation>" ROW "<path_to_temporary_output>"
# then by COLUMN
wb_command -cifti-parcellate "<path_to_temporary_output>" "<path _to_parcellation>" COLUMN "<path_to_final_output>"

Not sure how MRTrix data nii looks like, maybe you will have to also do a wb_command -cifti-transpose at the end. wb_command comes from HCP Connectome Workbench (Connectome - Workbench Commands). Software is already installed in the QuNex container, so you could also just enter the container and use it in there. If you need help here, let me know.

Best, Jure

5

Ok! Thank you very much!

Karin