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help > RE: Surface ROIs
Mar 7, 2017 02:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Surface ROIs
Dear Sami,
Sorry it was not very clear, yes you may use directly your subject-specific .mgz ROI files (e.g. when entering your ROIs using the GUI simply check the 'subject-specific' checkbox in the Setup.ROIs tab and then select all subjects, select all your ROI files, and click on 'select' to simultaneously enter all those subject-specific files -one file per subject-). When doing this simply make sure that the 'extract ... from functional dataset #' field for this ROI is set appropriately (e.g. if this ROI is going to be extracting the BOLD signal from dataset-2 just make sure that your dataset-2 in Setup.functional actually points to the functional data in subject-space; i.e. in the same space as your ROI file for each subject). This procedure works for any arbitrary set of subject-specific ROIs. The linked posts were just referring to an alternative way to enter subject-specific ROIs when those ROIs are derived from freesurfer (the alternative procedures avoid having to resample your ROIs to each subject anatomy, by having CONN explicitly use the freesurfer-generated lh|rh.sphere.reg files to learn the specifics of each subject anatomy)
Hope this helps
Alfonso
Originally posted by Sami Abboud:
Sorry it was not very clear, yes you may use directly your subject-specific .mgz ROI files (e.g. when entering your ROIs using the GUI simply check the 'subject-specific' checkbox in the Setup.ROIs tab and then select all subjects, select all your ROI files, and click on 'select' to simultaneously enter all those subject-specific files -one file per subject-). When doing this simply make sure that the 'extract ... from functional dataset #' field for this ROI is set appropriately (e.g. if this ROI is going to be extracting the BOLD signal from dataset-2 just make sure that your dataset-2 in Setup.functional actually points to the functional data in subject-space; i.e. in the same space as your ROI file for each subject). This procedure works for any arbitrary set of subject-specific ROIs. The linked posts were just referring to an alternative way to enter subject-specific ROIs when those ROIs are derived from freesurfer (the alternative procedures avoid having to resample your ROIs to each subject anatomy, by having CONN explicitly use the freesurfer-generated lh|rh.sphere.reg files to learn the specifics of each subject anatomy)
Hope this helps
Alfonso
Originally posted by Sami Abboud:
Dear Alfonso,
Thank you for the your answer.
If I understood well from reading the two previous posts you mentioned, it seems that I cannot define ROIs from subject-space but only from fsaverage space. Is that so?
What I have as input is a surface overlay file that is created by morphing a specific atlas to each and every single subject (relying on the subject-specific anatomy).
Should I then morph this overlay to fsaverage to be able to using CONN's analysis pipeline?
Cheers,
Sami
Thank you for the your answer.
If I understood well from reading the two previous posts you mentioned, it seems that I cannot define ROIs from subject-space but only from fsaverage space. Is that so?
What I have as input is a surface overlay file that is created by morphing a specific atlas to each and every single subject (relying on the subject-specific anatomy).
Should I then morph this overlay to fsaverage to be able to using CONN's analysis pipeline?
Cheers,
Sami
Threaded View
| Title | Author | Date |
|---|---|---|
| Sami Abboud | Feb 27, 2017 | |
| Alfonso Nieto-Castanon | Mar 1, 2017 | |
| Justyna Beresniewicz | Oct 5, 2018 | |
| Daniel Berge | Oct 5, 2018 | |
| Sami Abboud | Mar 1, 2017 | |
| Alfonso Nieto-Castanon | Mar 7, 2017 | |