Hi Ikko
> 1. I tried to make seed*seed matrices as follows, and now I'm waiting for the result to come. Is this argumentation correct?
>
> probtrackx2
> -s /fsl_course_data/fdt2/subj1.bedpostX/merged
> -m /fsl_course_data/fdt2/subj1.bedpostX/nodif_brain_mask
> -x /fsl_course_data/fdt2/subj1.bedpostX/struct.nii.gz
> --omatrix1
> --forcedir /TEST_matrix1_2014_7_5
> --network
> --xfm /fsl_course_data/fdt2/subj1.bedpostX/xfms/str2diff.mat
You do not need the —network flag. By the way what is the "struct” image that is used as a seed? Does this contain the whole structural? —omatrix1 will produce a NxN matrix, where N the number of voxels in your seed. If you have included the whole structural, N will be too large and it can take days to compute (and a large amount of memory). We normally use the —omatrix1 option by choosing a subset of voxels (for instance voxels at the GM/WM interface).
> 2. I'd also like to make matrices from free_surfer_label, and I've got free_surfer_label already. What else should I do?
Yes, you can use surfaces as seeds, the matrix will then count between surface vertices rather than voxels. See the probtrackx documentation for handling FreeSurfer surfaces.
> 3. Can I make such matrices also from AAL_labels? If it is possible, are there anything I should do before doing protrackx2?
Yes, you can define the seed ROIs in a text file and then use the —network mode.
Cheers
Stam
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