open-discussion > Surface based functional connectivity using Freesurfer- problem
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Jul 30, 2019  02:07 PM | S. Al-Wasity - University of Glasgow
Surface based functional connectivity using Freesurfer- problem
Dears
I am try to perform group analysis of resting state functional connectivity in surface level. But I am having a problem somewhere!
I followed the steps in these threads (https://www.nitrc.org/forum/forum.php?th...
https://www.nitrc.org/forum/forum.php?th...
https://www.nitrc.org/forum/message.php?...
https://www.nitrc.org/forum/message.php?...
https://www.nitrc.org/forum/forum.php?th...), and my pipeline was as following:

1- Setup.Structurals tab: for each subject, I selected the anatomical file generated by freesurfer (subj**/freesurfer/mri/brainmask.mgz).
2- Setup.Functional tab: for each subject, I selected the functional scan (subj**/****.nii), and then I ran the preprocessing pipeline for surface-based analysis (in subject space) (without the structural segmentation step).
3- Setup.Options tab: Set the 'Analysis space' to (Surface: same as template(Freesurfer fsaverage).
4- Setup.ROIs tab: remove the MNI-space default ROIs and instead I loaded subject-independent fsaverage-space (lh.aparc.annot). and change the field '''extract ... from functional dataset #4 (Surface-Based data)'''.
5- In Setup tab, hit Done, then in the Denoising tab hit Done again.
6- Then in Analysis (1st-level)> Seed-to-Voxel/ ROI-to-ROI: Most of the seeds/Sources have no time series as shown in the attached image

However, in step (4) above, if I upload the subject specific (subj**/freesurfer/mri/aparc+aseg.mgz) file (after copying without any changes the system's FreeSurferColorLUT.txt file into the subject-specific folders and renaming it as aparc+aseg.txt), I will get the ROIs time series as shown in the attached image.

Any idea on how to solve this issue?

Sincerely
Salim
Attachment: Capture2.PNG