Hello FSL experts,
I have ran probtrackx2 with a list of masks (corresponding to AAL regions) both as seeds and targets, using --omatrix3 and --target3 options.
Now, I would like to normalize the third value of fdt_matrix3 (streamline count), in order to get an estimate of the connection probability. What is the best way to do this?
Also, I want to construct a ROI x ROI matrix, so I grouped the values of fdt_matrix3 for the respective ROIs (using the file coords_for_fdt_matrix3) and calculated the mean. Is this the best way to do this? And should I normalize before or after calculating the mean?
Here is the command that I used to run probtrackx:
probtrackx2 -s ${SUBJECT_DIR}/merged -m ${SUBJECT_DIR}/nodif_brain_mask.nii.gz -x seeds_multiple_masks.txt -l -P 5000 -V 0 --opd --omatrix3 --target3=seeds_multiple_masks.txt
Best regards,
Ana
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