Extracting DTI indices of segmented nuclei from FSL atlas

1

Dear MRTrix experts,

Thank you for the effort and time in developing MRTrix.

I am currently trying to extract the DTI indexes (AFD, FA, etc.) of my ROIs, which are segmented nuclei from FSL atlas.

However, I encountered this issue of dimension mismatch between my ROIs and DTI values. I attained the DTI values with tensor2metric.

Question 1

I noted the reply in a post on the MRTrix forum: Extracting ROIs for fixel-based analysis

I understand that DTI indexes are stored as fixel while my segmented nuclei are 3D images in voxel, hence the dimension mismatch. I also understand that to overcome this issue, I can first convert my 3D images into fixel by using voxel2fixel.

However, I have difficulties attempting the voxel2fixel successfully. The function is:

voxel2fixel [ options ] image_in fixel_directory_in fixel_directory_out fixel_data_out

May I have your help on what should I input for the four arguments of this function? What do they mean separately? I noted that there are only few posts about the actual example on running this function.

Question 2

May I know if there is another way in attaining the DTI indexes from my segmented nuclei?

Thank you for your time.

Best regards
Arthur

2 Likes
2

Hi Arthur,

I understand that DTI indexes are stored as fixel

No, DTI indices are purely voxel-wise in nature. Fixel-based commands should not need to be invoked at all if dealing purely with the tensor model.

More likely the dimension mismatch has arisen from determining the segmentation masks on a different image grid to that of the DWIs. This can be investigated by running mrinfo on each of the images you are working with. If this still does not provide enough information, you could try posting the results of mrinfo here, along with any screenshots that may help to communicate the issue.

Rob