Re: [HCP-Users] A minor question regarding HCP 7T movie data

for the "v2" version. This was done > in order to make that final 83 second clip begin precisely at the start of > the next TR for all 4 movie sessions. > > Given HRF variability, ignoring this change will probably not adversely > impact most analyses. > > -Keith > >

[HCP-Users] A minor question regarding HCP 7T movie data

Hi, The HCP S1200 Reference Manual says that there are two versions of 4 movie files. Some subjects have been scanned with one version, and the remaining subjects have been scanned with another version. Version 2 includes these changes: 7T_MOVIE1_CC1_v2 remains unchanged. 7T_ MOVIE2_HO1_v2

Re: [HCP-Users] Group-averaging of task fMRI data

--- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://www.google.com/maps/search/660+South+Euclid+Ave?entry=gmail=g>. > Tel: 314-747-617

[HCP-Users] Group-averaging of task fMRI data

Hi, For a group of subjects (e.g. 100 subjects in HCP S1200), we want to generate a group-average Cohen’s d map for a particular contrast in the working memory task. For this, we take level2 “cope1.dtseries.nii” file in cope20.feat folder of all those subjects, merge them using -cifti-merge, then

[HCP-Users] Local Gyrification Index

Hi, Does HCP database have Freesurfer-derived LGI for all 1200 subjects? Best, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] wb_command -metric-tfce

x 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Saturday, A

[HCP-Users] wb_command -metric-tfce

Hi, We have curvature data from two groups of subjects in a common anatomical space (MSMAll). We performed a univariate comparison between the two groups using t-test. We now have a map, which shows vertex-wise curvature difference between the two groups (the curvature difference is shown only

Re: [HCP-Users] S1200 MSMSulc files

les. > > Matt. > > From: Reza Rajimehr > Date: Thursday, March 21, 2019 at 6:34 PM > To: Matt Glasser > Cc: hcp-users > Subject: Re: [HCP-Users] S1200 MSMSulc files > > Thanks Matt! > > In the fsaverage_LR32k folder of one subject, we have two versions

Re: [HCP-Users] S1200 MSMSulc files

those files from individual MSMSulc files? Thanks, Reza On Thu, Mar 21, 2019 at 11:09 PM Glasser, Matthew wrote: > MSMSulc might not have a specific registration tag, did you check for such > files? > > Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com&

[HCP-Users] S1200 MSMSulc files

For a control analysis, we would like to have access to the following files: 32k MSMSulc files for curvature, thickness, and myelin (individual subjects and group average) The current S1200 release only has the MSMAll files. How can we have access to the MSMSulc files? Thanks, Reza

Re: [HCP-Users] Confusion about Destrieux labels

S_temporal_transverse) in the > gifti file. I would expect that the freesurfer outputs already contain 75 > labels. > > Tim > > > On Fri, Feb 22, 2019 at 12:08 PM Reza Rajimehr wrote: > >> Hi, >> >> We have loaded Destrieux parcellation of one of the HCP su

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

(and > -cifti-create-dense-from-template respects subcortical structure boundaries > when the input is cifti, so you would need a small script involving > -cifti-separate if you wanted a full in-order FOV representation of the > voxels). > > Tim > > > On Tue, Nov 20, 2018 at 6

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

Sorry ... I should have said 20 vertices difference. On Tue, Nov 20, 2018 at 3:52 PM Reza Rajimehr wrote: > ... 29716 indices in RH and 29696 indices in LH of cifti file. > > > On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote: > >> But there are 10 more vertices in

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

... 29716 indices in RH and 29696 indices in LH of cifti file. On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote: > But there are 10 more vertices in right hemisphere than left hemisphere ... > > > On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew > wrote: > >> Left

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

But there are 10 more vertices in right hemisphere than left hemisphere ... On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew wrote: > Left and right are registered. > > Matt. > > From: Reza Rajimehr > Date: Tuesday, November 20, 2018 at 2:04 AM > To: Matt Glasser > C

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

mstances, basically if spatial relationship > information must be obtained in software without full cifti support, > without leaving the cifti format). > > Tim > > > On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr wrote: > >> Thanks! The file that we looked into was a

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

n Essen et al 2012 Cerebral Cortex. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Monday, November 19, 2018 at 2:57 PM > To: Reza Rajimehr > Cc: hcp-users > > Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti > files &g

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

gt; hemispheres, and used early on, and for ongoing compatibility we stayed > with the same masks. > > Tim > > > On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr wrote: > >> We successfully used -cifti-export-dense-mapping to get the mapping from >> cifti indices

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+So

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Friday, November 16, 2018 at 1:17 PM > *To: *

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

gt; Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com> > Date: Friday, November 16, 2018 at 10:17 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Number of cortical vertices in cifti and gifti files > > Hi, > > A cifti fi

[HCP-Users] Number of cortical vertices in cifti and gifti files

Hi, A cifti file has 91282 vertices/voxels, a combined LR cifti file has 59412 vertices, and an individual hemisphere gifti file has 32492 vertices. So the number of cortical vertices in cifti files is less than the number of cortical vertices in gifti files (left hemi vertices + right hemi

Re: [HCP-Users] Questions about sulc, curvature, and thickness files

orrThickness has the curvature >regressed out. > > Peace, > > Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com> > Date: Monday, November 5, 2018 at 2:48 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Quest

[HCP-Users] Questions about sulc, curvature, and thickness files

Hi, 1) The Sulc maps in HCP seem to be similar to the sulcal depth maps in Freesurfer; both show major sulci. Is there any detailed information on how these maps are obtained? 2) What is the type of curvature in the Curvature files of HCP? Mean curvature or Gaussian curvature? 3) There are two

Re: [HCP-Users] Question about dense functional connectome

e, -cifti-parcellate on the dtseries, > and then do the correlations on the parcellated timeseries, rather than > averaging correlations together). > > Tim > > > On Thu, Oct 25, 2018 at 10:20 AM, Reza Rajimehr > wrote: > >> Thanks Matt! Looks like -cifti-restrict-dense-map c

Re: [HCP-Users] Question about dense functional connectome

ps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Thursday, October 25, 2018 at 3:17 AM > *To: *"Glasser, Matthew&q

Re: [HCP-Users] Question about dense functional connectome

, Reza On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew wrote: > Use swap space. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Wednesday, October 24, 2018 at 4:57 PM > To: Reza Rajimehr > Cc: "hcp-users@humanconnectome.org" > Subje

[HCP-Users] Question about dense functional connectome

Hi, We are trying to unzip and load dense functional connectome (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip or HCP_S900_820_rfMRI_MSMSulc_groupPCA_d4500ROW_zcorr.zip from