Hi
If you mean how you can get a connectivity matrix from a group of ROIs using tractography, you can use the probtrackx2 tool.
For example, say you have rois A, B and C and you want a 3x3 connectivity matrix. You can use the following pseudo-code:
echo ROI_A.nii.gz > seeds.txt
echo ROI_B.nii.gz >>seeds.txt
echo ROI_C.nii.gz >>seeds.txt
probtrackx2 --network --omatrix1 --seed=seeds.txt [+other options]
The output of interest to you will be an ASCII text file called fdt_network_matrix which in this case is a 3x3 matrix containing the number of streamlines that start from ROI i and end up in ROI j.
I would recommend going through the FDT documentation (particularly BedpostX and probtrackx) if you are not familiar with these tools.
Cheers
Saad
Hello,
I'm trying to perform a structural connectivity analysis using the Brain Connectivity Toolbox, which requires a network matrix as input. I have DTI data that was processed through FSL, and I was wondering:
(1) Can I use FSL's FDT command to obtain the connectivity matrices I would need?
(2) What is the best way to use this command to produce connectivity matrices?
(3) Is there a recommended alternative method?
Thank you!
Kelly
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Saad Jbabdi, PhD
Associate Professor
MRC Career Development Fellow
FMRIB Centre, University of Oxford,
John Radcliffe Hospital, Oxford, OX3 9DU, UK.
tel (+44)1865-222466 (fax 717)
