Hi Joelle, You should be aware of potential issues with using anatomically-defined ROIs for rfMRI network analysis.
Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., Webster, M., Beckmann, C. F., Nichols, T. E., et al. (2011). Network modelling methods for FMRI. NeuroImage, 54(2), 875–891. http://doi.org/10.1016/j.neuroimage.2010.08.063 Gordon, E. M., Laumann, T. O., Adeyemo, B., Huckins, J. F., Kelley, W. M., & Petersen, S. E. (2014). Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cerebral Cortex. http://doi.org/10.1093/cercor/bhu239 --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Neuroscience Phone: 314-362-7864 Email: gburg...@wustl.edu > On Dec 15, 2015, at 11:24 AM, Joelle Zimmermann > <joelle.t.zimmerm...@gmail.com> wrote: > > Hi Michael, > > Thanks! So currently, the 2 available parcellation schemes are the Freesurfer > Desikan-Killiany (aparc+aseg.mgz) and Destrieux (aparc.a2009s+aseg.mgz) in > the structural extended preprocessed/T1w/mri folder? Im presuming these are > in the subject's T1 individual subject space. > > Are you aware whether these parcellation schemes are already available in the > MNI standard space? The goal is to parcellate the functional BOLD data (which > are currently in MNI standard space; Ie in the FIX extended package, the > MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii). Or > alternatively, if you could point me to where the volumetric functional BOLD > data in T1 space is (I cannot locate it in the FIX extended package - this > only seems to have func already normalized to MNI), I could directly apply > the aparc+aseg parcellation (that's in T1 space) to this. > > Thanks, > Joelle > > > > On Tue, Dec 15, 2015 at 10:46 AM, Harms, Michael <mha...@wustl.edu> wrote: > > Hi, > The only purely anatomical parcellation that is available currently are those > provided by FreeSurfer, which you seem to be familiar with. > > If you are interested in a functional parcellation, there is the Gordon et > al. parcellation derived from non-HCP rfMRI data. A parcellation that > incorporates the myelin maps and rfMRI data and which is specifically derived > from a subset of HCP participants is in the works (from Matt G.) > > 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: Tuesday, December 15, 2015 9:35 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] ROI parcellation > > Hi everyone, > > Does HCP have a specific ROI parcellation that is commonly used/recommended? > I would prefer to begin with anatomically (rather than functionally defined) > ROIs. > > My goal is to parcellate the voxel-wise time series into larger ROIs. I've > previously used the Desikan-Killiany atlas, but ideally would be interested > in using something with a finer parcellation. > > The only HCP parcellation I was able to find was the parcellation from the > ICA decomposition (resulting in one timeseries per ICA component), with 25, > 50, 100, 200, 300 components. However, I don't think this is something I am > interested in, as a single node (ie component) may comprise voxels that are > scattered across the brain. > > Is there anything like an anatomical ROI parcellation that's typically used > by HCP people? > > Thanks, > Joelle > > > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
