If you want connectivity matrices based on a parcellation that respects the cortical surface, then you'll need to use the CIFTI data, and you'll need a parcellation to go along with it that is also based on the surfaces (for the cortical grayordinates).
We would definitely suggest that you go this route, since much of the HCP effort, from acquisition through processing, is designed around surface-based analyses of the cortical data.
Also, you probably want to use the "FIX" cleaned data, which has "*clean*" in the file name, rather than just the minimally pre-processed .dtseries.nii.
I think the basic file types are well documented in the release documentation.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com>
Date: Wednesday, November 25, 2015 2:40 PM To: Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI Hi Tim,
Thanks for your response. Within the Resting State fMRI 1 preprocessed in the 500 Subjects + MEG2, I see the rfMRI_REST1_LR.nii.gz, which I presume is the Nifti-1 data. And then I see an rfMRI_REST1_LR_Atlas.dtseries.nii
- Is that the dtseries.nii Cifti you refer to? Could you explain a bit more about what's special about the Cifti file? I understand it Cifti is able to handle surface vertices and subcortical voxels in one file (i.e. gray ordinates).
My ultimate goal is to parcellate the brain into cortical regions of interest, in order to ultimately look at regional functional connectivity matrices. Do I need the dtseries.nii cifti for that? It seems like the advantage of that is having surface vertices
(i.e. knowing the precise shape of the surface of the brain) - which I don't think I need for a standard FC matrix...
Thanks,
Joelle
On Tue, Nov 24, 2015 at 6:16 PM, Timothy Coalson
<tsc...@mst.edu> wrote:
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- [HCP-Users] CIFTI and NIFTI -parcellating rfMRI Joelle Zimmermann
- Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI Timothy Coalson
- Re: [HCP-Users] CIFTI and NIFTI -parcellating r... Joelle Zimmermann
- Re: [HCP-Users] CIFTI and NIFTI -parcellati... Harms, Michael
- Re: [HCP-Users] CIFTI and NIFTI -parcel... Timothy Coalson
- Re: [HCP-Users] CIFTI and NIFTI -p... Joelle Zimmermann
- Re: [HCP-Users] CIFTI and NIFT... Glasser, Matthew
- Re: [HCP-Users] CIFTI and NIFT... Timothy Coalson