Re: [HCP-Users] questions about the preprocessing for HCP fMRI data

[Glasser, Matthew]

We used the 2mm nonlinear template from FSL.  While you can use things like the atlases you mention, you should not believe they represent functional units of the cortex.   The closest thing to that currently available would be something like the Yeo or Power et al functional network parcellations.  One could split the spatially contiguous pieces of the surface-based 17 network Yeo et al parcellation into roughly 50 parcels per hemisphere.  The next version of Connectome Workbench command line tools will have something that makes this easier to do.  Also, we hope to have parcellations based on the HCP data in the future.  As for subcortical structures, the FreeSurfer segmentation is already available to you, and for the cerebellum or striatum the FreeSurfer group has some finer resting state parcellations available.   Peace, Matt. From: Hai Shu <hai...@umich.edu> Date: Saturday, March 15, 2014 11:49 PM To: Matt Glasser <glass...@wusm.wustl.edu> Subject: questions about the preprocessing for HCP fMRI data Dear Matthew Glasser, I am a PhD student of University of Michigan Department of Biostatistics. I have some questions about the MNI template you used for the Human Connectome Project (HCP) resting-state fMRI data as follows. Hope get your kind help. (1) Which MNI 152 template you used for the rfMRI data? The nonlinear or the linear one?I see many MNI 152 templates in the website http://www.bic.mni.mcgill.ca/ServicesAtlases/HomePage which is led from the FSL website http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases (2) Do you have any corresponding structural atlas for the rfMRI data? From the atlas, I hope to know which voxels belong to a certain Brodmann's area or a subcortical region like hippocampus. If any, could you please share it with me? (3) If you did not have such a structural atlas in question (2), could I use the Harvard-Oxford cortical and subcortical structural atlases distributed with FSL. See http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases It seems they used the linear MNI 152 template, and I find that the HCP preprocessed rfMRI data is not perfectly co-registered with the Harvard-Oxford atlas. So the question goes back to the question (1). Looking forward to your reply. I will appreciate it. Thanks. Best regards, Hai Shu PhD Candidate Department of Biostatistics University of Michigan, Ann Arbor   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