er of streamlines (as the more streamlines,
the more robust the distance measure).
Peace,
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, October 6, 2017 at 7:30 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "
;hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Tuesday, October 3, 2017 at 6:30 PM
To: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkar
om the biological mechanism as Tim says.
There’s more discussion of this in the paper I referenced.
Peace,
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, October 6, 2017 at 5:30 PM
To: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mai
Hi,
I’m working with the Glasser multi-modal parcellation and I’d like to know if
there is some prevalent notion of distance between any two surface ROIs in the
parcellation? If there is, could you please tell me how I could obtain it or
point me to a source?
Thanks a lot!
Regards,
Karthik
Thanks a lot, Matt! I just saw Stam's email and responded as well.
Regards,
Karthik
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Friday, September 1, 2017 5:07:25 PM
To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP
--os2t --s2tastext
Regards,
Karthik
From: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>
Sent: Friday, September 1, 2017 4:40:46 PM
To: Glasser, Matthew
Cc: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP
for a right-hemisphere ROI.
Now these .gii files are the ones I provide to probtrackx.
Regards,
Karthik
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Friday, September 1, 2017 4:30:31 PM
To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP
ishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation
Are all of these files in ${StudyFolder}/${Subject}/T1w?
Matt.
From: "Gopalakrishnan, Karthik"
<gkart...@gatech.edu<mailto:gkart...@gatech.edu>>
Dat
7 4:14:03 PM
To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation
Which white matter surface are those on? I assume the bedpostX data are what
we released?
Peace,
Matt.
From: "Gopalakrishnan, Karth
The file white-masks.txt and the file targets.txt contain newline-separated
paths to each of the 360 ROIs (.gii files).
Thanks!
Karthik
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Friday, September 1, 2017 4:06:15 PM
To: Gopalakrishnan, Karthi
/merged -m ../Diffusion.bedpostX/nodif_brain_mask --dir=L1
--targetmasks=targets.txt --os2t --s2tastext
Thanks!
Karthik
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Friday, September 1, 2017 8:16:51 AM
To: Gopalakrishnan, Karthik; HCP-Users@humanconnecto
Hi all,
I ran probtrackx for HCP subject 100206 using the MMP1.0 Glasser surface ROIs.
My seeds in each ROI are at the white matter-gray matter boundary. I ran
probtrackx in network mode as well as seed-to-ROI mode for the subject, and I
applied the method described in
Hi Jenn,
Have any last-minute issues come up or is the S1200 release including the
bedpostx data going to happen this week?
Thanks!
Karthik
From: hcp-users-boun...@humanconnectome.org
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Elam, Jennifer
Sent: Monday, February 13, 2017
7 at 6:36 PM, Gopalakrishnan, Karthik
<gkart...@gatech.edu<mailto:gkart...@gatech.edu>> wrote:
Thanks Niels and Moises!
Niels, the documentation in the Github repo makes setting up the overlay look
pretty straight-forward. I did take a look at some of the code – it looks like
the fsl_sub script
: Tuesday, January 31, 2017 4:19 AM
To: Gopalakrishnan, Karthik <gkart...@gatech.edu>
Cc: Moises Hernandez Fernandez <mois...@fmrib.ox.ac.uk>;
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Running bedpostx on HCP diffusion data
Hi Karthik,
You may find this useful for getting
data? And on a slightly different note, what
kind of memory usage should I anticipate when I run this for HCP diffusion data?
Regards,
Karthik
From: Moises Hernandez Fernandez [mailto:mois...@fmrib.ox.ac.uk]
Sent: Friday, January 27, 2017 3:37 PM
To: Gopalakrishnan, Karthik <gkart...@gatech.edu&
ois...@fmrib.ox.ac.uk>; Gopalakrishnan,
Karthik <gkart...@gatech.edu>
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Running bedpostx on HCP diffusion data
One should use 3 fibers for HCP data however.
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@h
Hi,
I want to run bedpostx on HCP diffusion data - what is the estimated time for
successfully running it for a HCP subject in a regular computer without a GPU?
Also, what are the recommended hardware specs to run bedpostx on HCP data?
Thanks!
Karthik
-metric-merge 180 times, each time
passing -column as the values in the integer set [1, 180]. Is this right?
Thanks!
Karthik
From: Timothy Coalson [mailto:tsc...@mst.edu]
Sent: Monday, October 24, 2016 4:49 PM
To: Gopalakrishnan, Karthik <gkart...@gatech.edu>
Cc: Glasser, Matthew
, October 21, 2016 4:14 PM
To: Gopalakrishnan, Karthik <gkart...@gatech.edu>; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii
You can convert the CIFTI file to a GIFTI label file using wb_command
-cifti-separate. As for going from GIFTI
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