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help > RE: Preprocessed fMRI data into CONN toolbox
Jun 20, 2016 07:06 PM | Alfonso Nieto-Castanon - Boston University
RE: Preprocessed fMRI data into CONN toolbox
Hi Talia,
Typically the way to perform surface-level analyses in CONN from FreeSurfer-processed data is the following:
1) in Setup.Structural enter the freesurfer-generated T1 files (e.g. T1.mgz in the subject-specific folders), and when prompted select 'Yes' if you also want CONN to automatically import the aseg gray/white/CSF masks computed by FreeSurfer
2) in Setup.functional enter the functional data for each subject that is coregistered to the above structural volumes
3) in Setup.Options select the 'fsaverage (surface-level analyses)' option in 'Analysis space'
Everything else will be defined in the same way as for volume-based analyses. Note that in Setup.ROIs you typically would also want to remove the MNI-space default ROIs included there and enter instead surface-based ROIs (e.g. FreeSurfer aparc files in fsaverage space). If you prefer to combine MNI-space ROIs with your surface-based analyses then typically you would want to define an additional MNI-space dataset in Setup.Functionals pointing to your MNI-normalized functional volumes and then make sure that the MNI-space ROIs are being extracted from that new dataset instead (e.g. select 'extract from dataset-2' for those ROIs in the Setup.ROIs tab), while the surface-based ROIs are being extracted from the original dataset (e.g. select 'extract from dataset-0' for those ROIs)
Hope this helps
Alfonso
Originally posted by Talia R:
Typically the way to perform surface-level analyses in CONN from FreeSurfer-processed data is the following:
1) in Setup.Structural enter the freesurfer-generated T1 files (e.g. T1.mgz in the subject-specific folders), and when prompted select 'Yes' if you also want CONN to automatically import the aseg gray/white/CSF masks computed by FreeSurfer
2) in Setup.functional enter the functional data for each subject that is coregistered to the above structural volumes
3) in Setup.Options select the 'fsaverage (surface-level analyses)' option in 'Analysis space'
Everything else will be defined in the same way as for volume-based analyses. Note that in Setup.ROIs you typically would also want to remove the MNI-space default ROIs included there and enter instead surface-based ROIs (e.g. FreeSurfer aparc files in fsaverage space). If you prefer to combine MNI-space ROIs with your surface-based analyses then typically you would want to define an additional MNI-space dataset in Setup.Functionals pointing to your MNI-normalized functional volumes and then make sure that the MNI-space ROIs are being extracted from that new dataset instead (e.g. select 'extract from dataset-2' for those ROIs in the Setup.ROIs tab), while the surface-based ROIs are being extracted from the original dataset (e.g. select 'extract from dataset-0' for those ROIs)
Hope this helps
Alfonso
Originally posted by Talia R:
Hi all,
I preprocessed my resting state data using FreeSurfer(specifically using FSFAST) and I'm curious to know if anyone has tried importing that kind of data into the CONN toolbox and which files to import to do first level and group level analyses. I like the connectivity images that are outputted using the CONN toolbox but I would prefer not starting from scratch by having the data preprocessed using SPM.
Does anyone have any idea about how I can potentially do this?
Thank you!
I preprocessed my resting state data using FreeSurfer(specifically using FSFAST) and I'm curious to know if anyone has tried importing that kind of data into the CONN toolbox and which files to import to do first level and group level analyses. I like the connectivity images that are outputted using the CONN toolbox but I would prefer not starting from scratch by having the data preprocessed using SPM.
Does anyone have any idea about how I can potentially do this?
Thank you!
Threaded View
| Title | Author | Date |
|---|---|---|
| Talia R | Jun 15, 2016 | |
| Alfonso Nieto-Castanon | Jun 20, 2016 | |
| Bruno Hebling Vieira | Mar 1, 2019 | |
| Alfonso Nieto-Castanon | Mar 6, 2019 | |
| Talia R | Jun 21, 2016 | |
| Alfonso Nieto-Castanon | Jun 21, 2016 | |
| Scott H | Mar 27, 2017 | |
| Alfonso Nieto-Castanon | Mar 27, 2017 | |
| Scott H | Mar 27, 2017 | |
| Alfonso Nieto-Castanon | Mar 27, 2017 | |