Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii

2016-10-21 Thread Glasser, Matthew 
You can convert the CIFTI file to a GIFTI label file using wb_command 
-cifti-separate.  As for going from GIFTI label to surf+label (probtrackx's 
interpretation of GIFTI), you'll need to use the label2surf.  Hopefully either 
one of the oxford folks can explain how to use that here or on the FSL list.

Peace,

Matt.

From: 
>
 on behalf of "Gopalakrishnan, Karthik" 
>
Date: Friday, October 21, 2016 at 2:12 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii

Hi all,

How do we convert a dlabel.nii file containing 180 ROIs 
(Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) 
to a surf.gii file? We want to do that such that the output ROIs can be used in 
probtracx.

Thanks!

Regards,
Karthik

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Re: [HCP-Users] gradient nonlinearity correction question

2016-10-21 Thread Keith Jamison 
FYI, when available, you can enable it on the scanner in the
"Resolution->Filter" tab with the "Distortion Correction" checkbox.  It's
often used for structural scans like MPRAGE, where you will see two DICOM
folders in the output:  and _ND.  ND means "No
Distortion [Correction]".. .A very confusing choice of acronym.  You can
then compare the online corrected (not _ND) and offline using gradunwarp.

-Keith


On Wed, Oct 19, 2016 at 4:44 PM, Glasser, Matthew 
wrote:

> Some do for some sequences, but because it is not uniformly applied and
> because they are likely not to use optimal interpolation algorithms, we
> prefer to do offline correction.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Antonin Skoch <
> a...@ikem.cz>
> Date: Wednesday, October 19, 2016 at 4:27 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] gradient nonlinearity correction question
>
> Dear experts,
>
> during the set-up of gradunwarp scripts, it came to my mind, why scanner
> vendors standardly do not perform gradient nonlinearity correction directly
> on the scanner as part of on-line image reconstruction system (i.e. ICE in
> Siemens)?
>
> Regards,
>
> Antonin Skoch
>
>
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> Healthcare Information or other information of a sensitive nature. If you
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> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
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Re: [HCP-Users] dense structural connectivity based on probabilistic tractography

2016-10-21 Thread Elam, Jennifer 
Hi Selen,

Neither tractography dense connectomes nor bedpostx processed datasets have yet 
been released. We do still plan to release these, but because of competing 
priorities and a new version of FSL's Eddy, we are still working on the 
diffusion processing. We expect to release some of this data with the 1200 
subjects release (~1100 with MR data) in the next couple of months and some 
more extensively processed diffusion data in 2017.


Best,

Jenn


Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Selen Atasoy 

Sent: Friday, October 21, 2016 9:54:11 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] dense structural connectivity based on probabilistic 
tractography

Hi,

I was wondering if a dense structural connectivity based on DTI tractography 
for group average or for individuals has been released already. In the 900 
subject group average data I could find a dense functional connectivity but not 
the structural connectivity.

I read that the bedpostx on the DTI data was planned to be published this year 
but couldn’t find any probabilistic tractography data for an individual or 
group average yet. So was wondering if either the probabilistic tractography or 
dense structural connectivity matrices have already been released or are 
planned to be released.

It certainly would be of great interest.

Best,
Selen


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[HCP-Users] dense structural connectivity based on probabilistic tractography

2016-10-21 Thread Selen Atasoy 
Hi,

I was wondering if a dense structural connectivity based on DTI tractography 
for group average or for individuals has been released already. In the 900 
subject group average data I could find a dense functional connectivity but not 
the structural connectivity.

I read that the bedpostx on the DTI data was planned to be published this year 
but couldn’t find any probabilistic tractography data for an individual or 
group average yet. So was wondering if either the probabilistic tractography or 
dense structural connectivity matrices have already been released or are 
planned to be released.

It certainly would be of great interest.

Best,
Selen


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