Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI

[Harms, Michael]

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: The .nii.gz files are nifti-1 volumes, while the .dtseries.nii files are Cifti files.  If you need spatial information, converting Cifti to nifti-1 is not the way to go about it, instead you could use wb_command -cifti-separate into metric (.func.gii, one per hemisphere) and volume files, or use whatever -cifti-* commands are applicable to what you want to do spatially. Tim On Tue, Nov 24, 2015 at 11:14 AM, Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> wrote: Hi all, I'm working with the 500subjects + MEG2 preprocessed Resting State fMRI 1 Preprocessed dataset. Is the data just standard voxel-wise Nifti (it indeed looks like Nifti-1), or is it in a Cifti format that I need to convert to Nifti? My goal is to parcellate this data into ROI's, and I have a script that does this based on voxel-wise data, but as I understand Cifti is in gray ordinates.  Thanks, Joelle _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users