[color=#000000]Hi Talia,[/color]
[color=#000000]Typically the way to perform surface-level analyses in CONN from FreeSurfer-processed data is the following:[/color]
[color=#000000]1) in [i]Setup.Structural[/i] 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[/color]
[color=#000000]2) in [i]Setup.functional [/i]enter the functional data for each subject that is coregistered to the above structural volumes[/color]
[color=#000000]3) in [i]Setup.Options [/i]select the 'fsaverage (surface-level analyses)' option in 'Analysis space'[/color]
[color=#000000]Everything else will be defined in the same way as for volume-based analyses. Note that in [i]Setup.ROIs [/i]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 [i]Setup.Functionals [/i]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 [i]Setup.ROIs [/i]tab), while the surface-based ROIs are being extracted from the original dataset [/color](e.g. select 'extract from dataset-0' for those ROIs)
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Talia R:[/i][quote]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![/quote]
[color=#000000]Typically the way to perform surface-level analyses in CONN from FreeSurfer-processed data is the following:[/color]
[color=#000000]1) in [i]Setup.Structural[/i] 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[/color]
[color=#000000]2) in [i]Setup.functional [/i]enter the functional data for each subject that is coregistered to the above structural volumes[/color]
[color=#000000]3) in [i]Setup.Options [/i]select the 'fsaverage (surface-level analyses)' option in 'Analysis space'[/color]
[color=#000000]Everything else will be defined in the same way as for volume-based analyses. Note that in [i]Setup.ROIs [/i]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 [i]Setup.Functionals [/i]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 [i]Setup.ROIs [/i]tab), while the surface-based ROIs are being extracted from the original dataset [/color](e.g. select 'extract from dataset-0' for those ROIs)
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Talia R:[/i][quote]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![/quote]