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help > RE: how to employ func.gii to perform surface-based FC analysis?
Feb 2, 2021 10:02 PM | Alfonso Nieto-Castanon - Boston University
RE: how to employ func.gii to perform surface-based FC analysis?
Hi Julian,
I have not tried this yet, but at least in principle, it should be just a matter of using conn_surf_gii2nii to convert the lh.func.gii and rh.func.gii files into a single NIFTI format func.surf.nii file similar to the one that is produced by CONN's own surface-based preprocessing pipeline, so you could then simply import these files into CONN for surface-based analyses without any additional preprocessing required.
There may be some difficulties involved, as CONN uses freesurfer high-resolution format (with 163842 vertices and 327680 faces per hemisphere), and I am not sure if fMRIPrep uses the same convention. If in doubt, if you could please share your lh/rh.func.gii files I will be happy to take a look and see if I can propose a simple way to import that into CONN.
Best
Alfonso
Originally posted by Julian Dronse:
I have not tried this yet, but at least in principle, it should be just a matter of using conn_surf_gii2nii to convert the lh.func.gii and rh.func.gii files into a single NIFTI format func.surf.nii file similar to the one that is produced by CONN's own surface-based preprocessing pipeline, so you could then simply import these files into CONN for surface-based analyses without any additional preprocessing required.
There may be some difficulties involved, as CONN uses freesurfer high-resolution format (with 163842 vertices and 327680 faces per hemisphere), and I am not sure if fMRIPrep uses the same convention. If in doubt, if you could please share your lh/rh.func.gii files I will be happy to take a look and see if I can propose a simple way to import that into CONN.
Best
Alfonso
Originally posted by Julian Dronse:
Hi everyone,
I'm wondering the same thing: How to import surface based functional data from fMRIPrep preprocessing, i.e. left and right hemisphere .gii files?
As I understood it you have to input T1 structural files from freesurfer preprocessing and functional files in subject space and run functional preprocessing using CONN's surface based pipeline. This makes preprocessing with fMRIPrep redundant - all you need is the freesurfer preprocessing of structural files.
Did I get it wrong?
Best wishes
Julian
I'm wondering the same thing: How to import surface based functional data from fMRIPrep preprocessing, i.e. left and right hemisphere .gii files?
As I understood it you have to input T1 structural files from freesurfer preprocessing and functional files in subject space and run functional preprocessing using CONN's surface based pipeline. This makes preprocessing with fMRIPrep redundant - all you need is the freesurfer preprocessing of structural files.
Did I get it wrong?
Best wishes
Julian
Threaded View
| Title | Author | Date |
|---|---|---|
| Li He | Jan 11, 2020 | |
| Julian Dronse | Feb 1, 2021 | |
| Alfonso Nieto-Castanon | Feb 2, 2021 | |
| Julian Dronse | Feb 3, 2021 | |
| Alex Kapadia | Feb 24, 2023 | |
| Alfonso Nieto-Castanon | Feb 3, 2021 | |
| Julian Dronse | Feb 3, 2021 | |