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Dear Maedeh,

All of the matrix options (matrix1, matrix2, and matrix3) will always give you a matrix of voxel/vertex by voxel/vertex and not ROIxROI. If you want to get the ROI by ROI connectivity (34x34 matrix in your case) you want the --network option. I don’t believe that this option is available from the GUI, so you will have to use the command line. 

So, your steps should be:
1. Create 34 separate NIFTI files, one for each of your ROIs. Each NIFTI file should contain 1 for voxels in the ROI and 0 for all other voxels.
2. Create a text file listing the filenames of all the 34 NIFTI files (1 line per file)
3. Run probtrackx with the list of ROI filenames as seed and the --network option enabled. The simplest command line would be something like
$ probtrackx2 -s <bedpostX directory>/merged -m nodif_brain_mask.nii.gz -x <text file listing ROIs> --network
Note that if your ROIs are still in structural rather than diffusion space, you will also have to include the transformation matrices and/or warp fields (using the --xfm and --invxfm option).

Good luck,

Michiel

On 22 Sep 2018, at 16:47, Maedeh Khalilian <[log in to unmask]> wrote:

Dear fsl experts,
I have an anatomical MRI parcellation and i want to register it on its equivalent dMRI in order to compute its connectivity matrix using probtrackx in fsl.The parcellation is the output of Freesurfer "aparc+aseg.mgz" which is converted into .nii form, "aparc+aseg.nii". i have used it as a target mask and i have also used white.nii as a seed mask.( i have chosen "single mask" , "termination mask " in fsl Data part  and i have also chosen matrix3 in fsl Options.
the first question is that i didn't know what to import as row space and column space matrixes when choosing Matrix3 option, so i imported "aparc+aseg.nii" again.
Actually my parcellation has 34 ROIs so i expected to have 34 elements with the number of fibres between each pair (at most 5000 )or sth like this, but when i read the "fdt_matrix3.dot" in MATLAB, i see 863808 elements !! and I'm completely confused.
Now my questions are:
1- Are the steps i have taken and my inputs correct?
2- What should i have imported as my row space and column space matrixes?
3- If the steps are right, why do i have such big number for the number of parcels?
I would be grateful if you could help me,
Best regards,
Maedeh,
 

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