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
1. Depends on your internet connection and how far you are from us.
2. The nucleus accumbens is segmented by FreeSurfer. Dunno about the others.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of hercp mailto:he...@uw.edu>>
Date: Friday, December 1, 2017 at 12:5
@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
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
"
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
: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
We don't support using ft_read_cifti for MRI data, as it currently has some
bugs. Also I am not sure what you mean by "remove noise."
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Ferdaus Kawsar
mailto:ferdaus.kaw...@gmail.com>>
Date: Tuesday, October 25, 20
What we used for HCP Young Adults on the customized Connectom scanner is
attached.
(Lifespan piloting used a different set of directions).
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washin
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.
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
I just forwarded something that should answer this. Apparently I’ve been giving some mis-information: FSL’s label2surf program doesn’t work with GIFTI, so one needs to use surf2surf .func.gii metric ROIs like this:
surf2surf -i ${Subject}.${Hemisphere}.white.surf.gii -o --values=${Subject}.$
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