Hi,
I think it is appropriate to comment/remind that “single-subject-specific 
version” in this context is still a group based (maximum probability) 
parcellation, just one that that has been projected to the volume using the 
subject specific surfaces.   True subject-specific parcellations, based on the 
areal classifier, will be available down the road, once we can get them 
generated for all subjects.

cheers,
-MH

--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
<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 11, 2016 at 2:56 PM
To: Peter McColgan <pmccolga...@qub.ac.uk<mailto:pmccolga...@qub.ac.uk>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Glasser nature atlas

You can get the help info of commands by running them with no arguments, or 
from here:

http://www.humanconnectome.org/software/workbench-command.php?function=-label-to-volume-mapping

Note that the ribbon mapping method (which is generally recommended when you 
have pial and white surfaces) of surface to volume mapping is "generous" in 
that it assigns values to voxels that are only partially inside the cortical 
ribbon - this can be dealt with if it is a problem for your use.

Tim


On Tue, Oct 11, 2016 at 2:11 AM, Peter McColgan 
<pmccolga...@qub.ac.uk<mailto:pmccolga...@qub.ac.uk>> wrote:


Thanks Matt, I am keen to generate a  single-subject-specific version using 
-cifti-separate and -label-to-volume-mapping, using the subject's own surfaces.


Could you advise how I go about doing this?


Thanks again for your help.


bw


Peter

________________________________
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: 11 October 2016 00:09:24
To: Peter McColgan; NEUROSCIENCE tim; Elam, Jennifer
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>

Subject: Re: [HCP-Users] Glasser nature atlas

 A number of people have been using this file: 
HCP_PhaseTwo/Q1-Q6_RelatedValidation210/MNINonLinear/fsaverage_LR32k/Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Peter McColgan 
<pmccolga...@qub.ac.uk<mailto:pmccolga...@qub.ac.uk>>
Date: Monday, October 10, 2016 at 3:22 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Elam, Jennifer" 
<e...@wustl.edu<mailto:e...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Glasser nature atlas


Thanks Tim, I have found a number of files at 
https://balsa.wustl.edu/sceneFile/show/L731 can I ask which is the best one to 
use for the nature paper parcellation?

Thanks

Peter


________________________________
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Sent: 04 October 2016 22:45:46
To: Elam, Jennifer
Cc: Peter McColgan; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Glasser nature atlas

Making a "nifti version" isn't a simple conversion, as some lengthy 
conversations on this list have elaborated on.

The good news: if you want a single-subject-specific version, that is possible, 
using -cifti-separate and -label-to-volume-mapping, using the subject's own 
surfaces.

The bad news: if you want it to be a group atlas, the currently popular volume 
registration methods aren't good enough at cortical area alignment to make our 
parcellation meaningful in a group-average volume space, and thus we do not 
recommend making a volumetric version in such a space.  In the meantime, 
surface registration avoids several difficulties inherent to volume 
registration, and was instrumental in being able to create the parcellation at 
all (via alignment of areal features).

For more detailed discussion:

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03078.html

Tim


On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer 
<e...@wustl.edu<mailto:e...@wustl.edu>> wrote:

Hi Peter,

The data for the new parcellation are available in the BALSA database, see this 
thread: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02876.html


We recommend using the included Connectome Workbench scene file to conveniently 
view the data in the wb_view part of the software platform. Get Connectome 
Workbench here: 
https://www.humanconnectome.org/software/get-connectome-workbench.html


Many of the files are in the CIFTI data 
format<http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-help>,
 which has a lot of advantages, but if you need NIFTI versions, you can use 
wb_command<http://www.humanconnectome.org/software/workbench-command.php> 
(distributed as part of Connectome Workbench) to do the conversion.


There's lots of help for using wb_command in the HCP-Users mail archive, and/or 
you could post more questions to the list.


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<tel:314-362-9387>
e...@wustl.edu<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>


________________________________
From:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Peter McColgan 
<pmccolga...@qub.ac.uk<mailto:pmccolga...@qub.ac.uk>>
Sent: Tuesday, October 4, 2016 9:29:30 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] Glasser nature atlas



Dear HCP team,


Is it possible to download a nifti version of the Glasser atlas featured 
recently in nature?


Thanks


bw


Peter

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