[HCP-Users] FIX-denoised

Hi everyone, I'm interested in using the FIX-denoised data, and am currently looking at the extended package, as I'm interested in the volumetric data. I'm wondering whether the motion parameters have already been regressed out from the FIX denoised rfMRI_REST1_LR_hp2000_clean.nii.gz? I'm

Re: [HCP-Users] FIX-denoised

below. > > -- > 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.

Re: [HCP-Users] FIX-denoised

>> >>if the FIX denoising worked as intended... Given that FIX will look for >> >>components that correlate with WM and CSF signal these signals are >> >>already regressed out if components were properly identified. The same >> >>is true for the physiol

Re: [HCP-Users] ROI parcellation

--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 > &g

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

he 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 file

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

ic (.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: > >&

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

t; wrote: > > > > It doesn’t matter what order you concatenate the data in, but I would > not recommend only analyzing the data of one phase encoding direction. > > > > Peace, > > > > Matt. > > > > From: <hcp-users-boun...@humanconnectome.org&

[HCP-Users] CIFTI and NIFTI -parcellating rfMRI

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

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

> Peace, > > Matt. > ________ > From: Joelle Zimmermann [joelle.t.zimmerm...@gmail.com] > Sent: Tuesday, November 24, 2015 11:14 AM > To: Greg Burgess > Cc: Glasser, Matthew; Elam, Jennifer; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] Phase Encoding left-to-ri

[HCP-Users] Demographic and behavioral subject data

Hello everyone, I want to pick a group of subjects from the 500 subjects +MEG2 for which I will perform (rsfMRI and dMRI) analysis. These should be young, healthy, subjects that have no abnormalities and cognitively able. Does anyone have any pointers about how I can go weeding out subjects?

Re: [HCP-Users] Demographic and behavioral subject data

id Avenue > St. Louis, MO 63110 > 314-362-9387 > el...@pcg.wustl.edu > www.humanconnectome.org > > > > *From:* hcp-users-boun...@humanconnectome.org [mailto: > hcp-users-boun...@humanconnectome.org] *On Behalf Of *Joelle Zimmermann > *Sent:* Monday, November 30, 2015 10

Re: [HCP-Users] Demographic and behavioral subject data

n-twins. > > Current Pregnancy > > Unsafe metal or devices in the body (Cardiac Pacemaker, cochlear implant, > aneurism clip) > > Moderate to Severe Claustrophobia > > > > Hope that helps. > > > > Best, > > Jenn > > > > Jennifer Elam, Ph

[HCP-Users] Has anybody done tractography on HCP diffusion data?

Hi - I'm a researcher at the McIntosh lab at the Rotman Research Institute. A few of us here are planning on working with HCP data. I was wondering whether anybody is working on (or aware of a group working on) fully preprocessing and tractography on HCP diffusion data, parcellated into some kind

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

atomy and Neurobiology, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > el...@pcg.wustl.edu > www.humanconnectome.org > > > > *From:* hcp-users-boun...@humanconnectome.org [mailto: > hcp-users-boun...@humanconnectome.org] *On Behalf Of *Glasser, Ma

[HCP-Users] Tractography on diffusion data for SC matrices

Hi Jennifer, I previously posted a question to the mailing list, and wanted to check with you as you may have a bit more of an insiders scoop. I was wondering whether tractography has been performed on the diffusion data for the end of creating structural connectivity matrices for individual

Re: [HCP-Users] Tractography on diffusion data for SC matrices

ol of Medicine > Department of Anatomy and Neurobiology, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > el...@pcg.wustl.edu > www.humanconnectome.org > > > > *From:* Joelle Zimmermann [mailto:joelle.t.zimmerm...@gmail.com] > *Sent:* Monda

[HCP-Users] Test-retest reliability / Intra vs inter subject variability of HCP data

Hi HCPers. I'm curious about the test-retest reliability and the inter subject versus intra subject variability of the HCP resting functional and diffusion data, particularly whether anyone has looked at this in SC and FC connectomes? To check this out in the rsFC data is simple, using the two

Re: [HCP-Users] Test-retest reliability / Intra vs inter subject variability of HCP data

h diffusion scan run twice (once each) with > >> different phase encode directions, you could analyze each of those > >> separately (only using the B0s from the opposite phase encode > >> direction). Then perform whatever test-retest tests you are interested > >

Re: [HCP-Users] global signal regression on HCP ICA FIX denoised BOLD?

that is at the discretion of each researcher afterwards? On Thu, Jan 5, 2017 at 12:00 PM, Stephen Smith <st...@fmrib.ox.ac.uk> wrote: > Yes,. > Cheers. > > > On 5 Jan 2017, at 11:57, Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> > wrote: > > Hi HCPers, > > Is it correct

[HCP-Users] global signal regression on HCP ICA FIX denoised BOLD?

Hi HCPers, Is it correct that global signal regression was not done on the ICA FIX denoised fmri BOLD data? Thanks, Joelle ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] comparison across acquisitions

data > had not been saved and could not be retroreconned. We advise using a > covariate of no interest for version number. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Joelle > Zimmermann <joelle.t.zimmerm...@gmail.com>

Re: [HCP-Users] comparison across acquisitions

n’t affected by this, just fMRI because diffusion was processed with the > same recon version (old scans were reprocessed). > > Peace, > > Matt. > > From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Wednesday, April 26, 2017 at 12:58 PM > To: Matt

[HCP-Users] comparison across acquisitions

Hi HCPers, I'm working with structural and functional connectomes from the S900 HCP. I'm wondering how the different acquisitions (ie Q1 Q2 etc) and releases would affect comparison across all SCs for example. Was data collected at different sites for example? - which may affect comparison across

Re: [HCP-Users] comparison across acquisitions

e. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Joelle > Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Thursday, April 27, 2017 at 1:50 PM > To: &qu

[HCP-Users] variation across connectomes

Hi HCPers, I'm looking at variation across SC and FC connectomes of subjects. I was wondering due to which variables we could potentially expect variability across subjects to arise? I've looked into acquisition, fmri reconstruction version, and age as potential factors of variation. Any other

Re: [HCP-Users] comparison across acquisitions

> > Peace, > > Matt. > > From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Wednesday, April 26, 2017 at 1:03 PM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> &

Re: [HCP-Users] variation across connectomes

interesting sources > of variance? > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Joelle > Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Friday, April 28, 2017 at 2:17 PM > To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] variation across connectomes

d Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Joelle > Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Saturday, April 29, 2017 at 10:30 AM > To: &quo

[HCP-Users] hcp publications

Hi HCPers, Is there a list out there of publications with HCP data ? I'm aware of the few main reference HCP publications, but looking beyond that... Thanks, Joelle ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] regression of potentially confounding variables

Hi HCPers, My goal is to look at variability of SC and FC across subject... I was wondering what would be recommended as regressors? In Stephen Smith's Nature Neuroscience 2015 paper looking at FC and cognition, the following was regressed: 1. Acquisition reconstruction software version (as an

[HCP-Users] motion parameters

Hi HCPers, I was wondering where I can find an average head motion parameter for each subject? Thanks, Joelle ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] question about link to behavioural measures docs

Hi HCPers, I am looking for a link to the documentation for citation for the following behavioural measures (see below). I had been referring to the following link, but it looks like that is now expired: