tions.
Best,
Heracles
From: Glasser, Matthew
Sent: Monday, January 01, 2018 4:30 PM
To: HERACLES PANAGIOTIDES ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] (no subject)
>From previous post:
There are four rfMRI runs per subject. LR vs RL refers to the phase encoding
direction and 1 and
LES PANAGIOTIDES mailto:he...@uw.edu>>
Date: Monday, January 1, 2018 at 6:26 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] (no subject)
Hi Matt and Happy New Year.
Is the processing already done and available on the site? If o, what are the
processed files
: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] (no subject)
Hello Matt,
I am getting ready to launch a group analysis of rfMRI files using Matlab. I
want to make sure that I am not making any fundamental errors in preprocessing.
I would be deeply appreciative, if I
I don’t know what the maximum capacity is.
Peace,
Matt.
From: hercp mailto:he...@uw.edu>>
Date: Friday, December 1, 2017 at 5:19 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] (no subject)
Thanks, Matt. I am in the Seattle area and plan to upgrade my spe
, 2017 at 12:58 PM
To: HUMAN CONNECTOME
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] (no subject)
Two questions:
1. What is the speed limit for downloading. I am planning to upgrade my
internet.
2. Does anyone know of a good ROI atlases that might include regions as the
Two questions:
1. What is the speed limit for downloading. I am planning to upgrade my
internet.
2. Does anyone know of a good ROI atlases that might include regions as the
substantia nigra, the nucleus accumbens, subdivisions of the hypothalamus, etc.
Heracles Panagiotides, PhD
_
@uw.edu>>
Cc: HUMAN CONNECTOME
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] (no subject)
rfMRI_REST1_LR_hp2000_clean.nii.gz is a volume file, not a cifti file. Cifti
files end in things like .dtseries.nii. See wb_command -cifti-help:
https://www.humanconnectom
rfMRI_REST1_LR_hp2000_clean.nii.gz is a volume file, not a cifti file.
Cifti files end in things like .dtseries.nii. See wb_command -cifti-help:
https://www.humanconnectome.org/software/workbench-command/-cifti-help
Tim
On Mon, Oct 23, 2017 at 4:17 PM, hercp wrote:
> I am running the command
I am running the command
wb_command -cifti-reduce rfMRI_REST1_LR_hp2000_clean.nii.gz MEAN mean.
rfMRI_REST1_LR_hp2000_clean.nii.gz
and I get this error returned:
ERROR: no cifti extension found in file C:/rfMRI_REST1_LR_hp2000_clean.nii.gz
Am I missing a step?
Thanks for your help,
Dear Heracles,
the development version of FreeSurfer now contains probabilistic labeling of
nuclei of Amygdala:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Regards,
Antonin Skoch
Hi Heracles,
There?s a very nice parcellated amygdala atlas based on HCP
The CalTech Atlas is an important step forward, but does have a few
limitations. Reading the paper is highly recommended. It is based on only
one hemisphere. Given how it was constructed, you may wish to
diffeomorphically warp to mni152 via ANTS or 3dQwarp. Take care when
decimating to EPI resoluti
Hi Heracles,
There’s a very nice parcellated amygdala atlas based on HCP data published by
Tyszka and Pauli (https://www.ncbi.nlm.nih.gov/pubmed/27354150). The atlas
dataset is accessible via http://evendim.caltech.edu/amygdala-atlas/ in various
spaces (MNI152 1mm and 700um and CIT168 700um) i
Does anyone know if there any atlases of amygdala subdivisions?
Heracles Panagiotides, PhD
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] (no subject)
I see asymmetries in the ventricles. Is this what you are referring to? Our
Radiologist looked at all of our subjects’ scans and didn’t note any issue.
Erin
On May 24, 2017, at 12:46 PM, Ariana Cahn
ma
I see asymmetries in the ventricles. Is this what you are referring to? Our
Radiologist looked at all of our subjects’ scans and didn’t note any issue.
Erin
On May 24, 2017, at 12:46 PM, Ariana Cahn
mailto:ac...@ualberta.ca>> wrote:
The brain is very asymmetric, so I was wondering if this ha
I do not have any flags for this subject from structural scan or surface QC
measures. What are you referring to specifically?
Erin
On May 24, 2017, at 11:44 AM, Ariana Cahn
mailto:ac...@ualberta.ca>> wrote:
Hello,
I was wondering if subject 130619 has been flagged in any way previously.
Tha
Hello,
I was wondering if subject 130619 has been flagged in any way previously.
Thanks,
--
*Ariana Cahn*
*BSc (Hons), *Neuroscience
*ac...@ualberta.ca *
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailm
:17 AM
> To: Matt Glasser
> Subject: Re: [HCP-Users] (no subject)
>
> Hi Matt,
>This is how I am removing noise from Volume file. Following is a
> AFNI command.
> 3dTproject -input rfMRI_REST1_AP.nii.gz -prefix rfMRI_REST1_AP_cleaned.nii.gz
> -ort rfMRI_RES
te: Tuesday, October 25, 2016 at 10:17 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] (no subject)
Hi Matt,
This is how I am removing noise from Volume file. Following is a
AFNI command.
3dTproject -input rfMRI_REST1_AP.nii.gz -prefix rfMRI_REST1_AP_cle
;
Date: Tuesday, October 25, 2016 at 12:31 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] (no subject)
Hi HCP Experts,
I need some help with resting analysis of m
Hi HCP Experts,
I need some help with resting analysis of my data. I
have extracted average time course for each sub-cortical parcels. I have
also extracted average time course for each cortical parcels (BA, aparc,
aparc.2009 and Glasser parcellation). For this I used
-cifti-
, October 14, 2016 at 8:30 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] (no subject)
Hi,
I am wondering if I can have the gradient table that HCP uses for dMRI?
Thank y
Hi,
I am wondering if I can have the gradient table that HCP uses for dMRI?
Thank you in advance,
Best wishes,
Maryam
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Inviato da Samsung Mobile.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
I am facing problems while uploading brain images onto 3D Slicer software. As
i try to load the image,the image gets inverted. Mapping is not
possible. KIndly provide me assistance.
Thank you
On 8/11/16, ARCHANA S wrote:
> I am facing problems while uploading brain images onto 3D software.
I am facing problems while uploading brain images onto 3D software. As
i try to load the image,the image gets inverted. Mapping is not
possible. KIndly provide me assistance.
Thank you
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lis
Yes, the preprocessed "Structural Extended" package for each subject has
the Freesurfer outputs that are intermediates in the HCP preprocessing
pipelines.
More info about the files output from the HCP pipelines that toy ate
unfamiliar worth is available in the HCP Reference Manual for the 900
Subje
Jenn wrote:
> output from the HCP pipelines that toy ate unfamiliar worth is available
Auto-complete run amok or typing while nursing? ;-)
A-reum, if you have the structural extended package, you'll find the freesurfer
subject directory here:
> /MyDataPath/subjectID/T1w/subjectID
Qdec should b
I don't know the name of the package, but it might be something like
"structural extended" -- one of them has the subject's freesurfer directory in
it.
On Dec 27, 2015, at 7:08 PM, A-reum Min wrote:
> hello
> my name is areum.
> i have some question to you.
> a few days ago i was down load H
hello
my name is areum.
i have some question to you.
a few days ago i was down load HCP(human connectom project) s900 data. -->
3T imaging protocol completed True ver.
but.. how can i use these HCP format.
i use a freesurfer software.
i have never seen before these format(fig.1.png) like a .gii , n
—
Sent from Mailbox
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Hi HCP-users,
I would like to draw an roi on the surface in native space and then after
obtaining those coordinates, convert that roi to functional space for later
processing in SPM. For example, I would like to draw an roi that
encompasses the voxels the hand notch of primary motor cortex. Then I
}.${Hemisphere}.roi.func.gii
Peace,
Matt.
From: Longchuan Li <leonad...@yahoo.com>
Reply-To: Longchuan Li <leonad...@yahoo.com>
Date: Monday, July 14, 2014 at 3:02 PM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] (no su
Hi, HCP experts
I have a question regarding transferring HCP border ROI file for surface-based
tractography in FSL. What I did were (1) draw a border roi; (2) transfer the
border ROI to a metric file; (3) transfer the metric file to a label file; (4)
transfer the label file to a surface file
Dear Sir or Madam,
I am new to the neuroimaging, and now I have a question about defining a
spherical seed region for the seed-based functional connectivity.
My question is:
If a seed region has a radius of 4 mm and is centered at MNI coordinates
(0,-53,26), and the voxel is 2-mm isotropic, what is
List conformation
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
alistairperry...@gmail.com
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
37 matches
Mail list logo
