Thanks Jennifer and Matt! On Tue, Dec 15, 2015 at 9:05 PM, Glasser, Matthew <[email protected]> wrote:
> We’ll have a multi-modally based parcellation for the MSMAll CIFTI data > soon. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Jennifer Elam < > [email protected]> > Date: Tuesday, December 15, 2015 at 3:51 PM > To: 'Joelle Zimmermann' <[email protected]>, "Harms, Michael" > <[email protected]> > Cc: 'Greg Burgess' <[email protected]>, "[email protected]" > <[email protected]> > > Subject: Re: [HCP-Users] ROI parcellation > > We have not distributed the Gordon et al. parcellation in any of the > released HCP data yet. There are CIFTI surface-based parcellations > available in both the Group Average and Connectome Workbench datasets > available on the HCP project page in ConnectomeDB: > https://db.humanconnectome.org/data/projects/HCP_900 as maps in the > RSN-networks.32k_fs_LR.dlabel.nii file – the 7 and 17 RSN network > parcellation from Yeo et al., JNP 2011 and the RSN network communities from > Power et al., Neuron 2011. > > > > Best, > > Jenn > > > > Jennifer Elam, Ph.D. > Outreach Coordinator, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > [email protected] > www.humanconnectome.org > > > > *From:* [email protected] [ > mailto:[email protected] > <[email protected]>] *On Behalf Of *Joelle Zimmermann > *Sent:* Tuesday, December 15, 2015 2:42 PM > *To:* Harms, Michael > *Cc:* Greg Burgess; [email protected] > *Subject:* Re: [HCP-Users] ROI parcellation > > > > Thank you Michael, I found those aparc+asegs there. > > > > Is the Gordon et al. parcellation available in the package? > > > > Greg, I'm aware of the advantages of the functional parcellation, it's > sort of a test run I'm starting off with the anatomical parcellations. > Thanks for the refs. > > > > Joelle > > > > On Tue, Dec 15, 2015 at 1:02 PM, Harms, Michael <[email protected]> wrote: > > > > Also, we encourage you to work in CIFTI-land so as to have a surface-based > analysis of the cortical data. But to answer your question, volumetric > versions of both those FS parcellations are available in each subject's > MNINonLinear folder; e.g., > > 100307/MNINonLinear/aparc+aseg.nii.gz > > 100307/MNINonLinear/aparc.a2009s+aseg.nii.gz > > > > Those particular files should be part of the standard Structural package. > > > > 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: [email protected] > > > > > > > > On 12/15/15 11:51 AM, "Greg Burgess" <[email protected]> wrote: > > > > 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: [email protected] > > > > On Dec 15, 2015, at 11:24 AM, Joelle Zimmermann < > [email protected]> 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 <[email protected]> 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: [email protected] > > From: Joelle Zimmermann <[email protected]> > > Date: Tuesday, December 15, 2015 9:35 AM > > To: "[email protected]" <[email protected]> > > 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 > > [email protected] > > 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 > > [email protected] > > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > HCP-Users mailing list > [email protected] > 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
