@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>
From: hcp-users-boun...@humanconnectome.org
on behalf of Pubuditha Abeyasinghe
Sent: Monday, July 30, 2018 12:38:51 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Tractogr
ttp://www.humanconnectome.org/>
From: hcp-users-boun...@humanconnectome.org
on behalf of Pubuditha Abeyasinghe
Sent: Monday, July 30, 2018 12:38:51 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Tractography data for the 1200 subject release
on behalf of Pubuditha Abeyasinghe
Sent: Monday, July 30, 2018 12:38:51 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Tractography data for the 1200 subject release
Hi HCP experts,
I am starting to work with the data from 1200 subject release.
I want to generate the connectome for all
, Matthew
Sent: Thursday, August 24, 2017 6:50 AM
To: hercp ; HUMAN CONNECTOME
Subject: Re: [HCP-Users] Tractography
Also as Steve has reminded me, you can download the Bedpostx outputs
pre-computed.
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of Matt Glasser
<g
ate: Thursday, August 24, 2017 at 6:53 AM
To: hercp <he...@uw.edu<mailto:he...@uw.edu>>, HUMAN CONNECTOME
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Tractography
That is the price one pays for really high spatial and angular
lt;he...@uw.edu<mailto:he...@uw.edu>>
Date: Thursday, August 24, 2017 at 6:31 AM
To: HUMAN CONNECTOME
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Tractography
Hello Everyone,
I am running BEDTPOSTX Estimation on FSL using DTI data
Hello Everyone,
I am running BEDTPOSTX Estimation on FSL using DTI data that I downloaded from
the HCP site. The process is taking a very long time (days) to process. Is
there a faster way to do tractography?
Thanks,
Heracles
___
HCP-Users
Hi Joelle and all,
we have a pipeline that takes diffusion MRI and T1-weighted data as input
and automatically computes structural connectivity matrices for arbitrary
cortical parcellations using three different connectivity metrics. It also
computes functional connectivity matrices from fMRI
Hi Jennifer,
That's good to hear! I don't have much experience with tractography, but it
looks like bedpostX creates all the files you need for running
probabilistic tractography (probabilistic tractography itself is run with
probtrackX for example). I suppose the probabilistic tractography is
Hi Joelle and all,
HCP does have running bedpostX on the diffusion data for HCP Subjects on our to
do list, but this data has not been released yet. We are hoping to have this
available to users by late winter/early spring 2016 after we release 7T data.
Best,
Jenn
Jennifer Elam, Ph.D.
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
are
normally the row and the targets the column).
Peace,
Matt.
From: Maarten Vaessen m.vaes...@gmail.com
Date: Wednesday, July 22, 2015 at 8:50 AM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
Subject: Re: [HCP-Users] tractography
Hi,
I did some more testing to see what could be the problem. The main weird thing I see is that in thecoords_for_fdt_matrix3 file, there are some strange values:
coords_for_fdt_matrix3 :
309 -57 38 0 8341
308 -57 38 0 8342
307 -56 38 0 8343
306
@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
The conversion was done like this:
wb_command -gifti-label-to-roi
../../MNINonLinear/fsaverage_LR32k/102816.L.aparc.a2009s.32k_fs_LR.label.gii
L.STS.func.gii -name S_temporal_sup
surf2surf -i
@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
Hi,
I did some more testing to see what could be the problem. The main weird thing I see is that in thecoords_for_fdt_matrix3 file, there are some strange values:
coords_for_fdt_matrix3 :
309 -57 38 0 8341
308 -57 38 0
Date: Sunday, July 19, 2015 at 12:03 PM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: FW: [HCP-Users] tractography
In this case: seed region to whole brain connectivity. The STS seed is
mainly for testing purposes
No I meant the dot convert.
Matt.
From: Maarten Vaessen m.vaes...@gmail.com
Date: Monday, July 20, 2015 at 3:29 AM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
The conversion was done
convert.
Matt.
From: Maarten Vaessen m.vaes...@gmail.com
Date: Monday, July 20, 2015 at 3:29 AM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
The conversion was done like
a seed of all white matter voxels with matrix3.
Peace,
Matt.
From: Maarten Vaessen m.vaes...@gmail.com
Date: Sunday, July 19, 2015 at 3:41 AM
To: Matt Glasser glass...@wusm.wustl.edu
Subject: Re: [HCP-Users] tractography
Hi Matthew,
I tried to use the file you suggested, and I can
: Wednesday, July 15, 2015 at 4:44 AM
To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] tractography
Hello,
I followed the guide lines below to create a dense connectome with probtrackx. I was just wondering how to proceed with converting the .dot file from
hi HCP,
we are trying to do tractography using FSL and HCP data. i have some questions
-- i suspect they have been answered already, but couldn't find those answers:
1. is there a file containing the grayordinate coordinates in the diffusion
space for a particular subject, both subcortical
Hi Matthew
As you noticed these are in-progress, therefore contain non-released pipelines
and code. We do not support unreleased code, but if you want I can send you a
binary (notice that we are still debugging/developing some aspects of this
pipeline).
Cheers
Stam
On 7 Apr 2015, at 10:03,
Hi all,
Sorry to hassle, but I haven’t had any answers for this yet – anyone have any
ideas?
Stam: maybe I should post this to the FSL list?
Cheers,
M@
On 25/3/15 9:19 , Matthew George Liptrot
matthew.lipt...@di.ku.dkmailto:matthew.lipt...@di.ku.dk wrote:
Hi,
I am trying to create some
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