Hi Matthew,
The aparc files Jenn meant are generated by Freesurfer, but we make them
available in cifti (*dlabel.nii) and gifti (*.label.gii) formats:
* 164k standard mesh
Structural_preproc/MNINonLinear/994273.aparc.164k_fs_LR.dlabel.nii
Structural_preproc/MNINonLinear/994273.aparc.a2009s.164k_fs_LR.dlabel.nii
Structural_preproc/MNINonLinear/994273.L.aparc.164k_fs_LR.label.gii
Structural_preproc/MNINonLinear/994273.L.aparc.a2009s.164k_fs_LR.label.gii
Structural_preproc/MNINonLinear/994273.R.aparc.164k_fs_LR.label.gii
Structural_preproc/MNINonLinear/994273.R.aparc.a2009s.164k_fs_LR.label.gii
* 32k standard mesh
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.aparc.32k_fs_LR.dlabel.nii
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.aparc.a2009s.32k_fs_LR.dlabel.nii
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.L.aparc.32k_fs_LR.label.gii
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.L.aparc.a2009s.32k_fs_LR.label.gii
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.R.aparc.32k_fs_LR.label.gii
Structural_preproc/MNINonLinear/fsaverage_LR32k/994273.R.aparc.a2009s.32k_fs_LR.label.gii
* native mesh
Structural_preproc/MNINonLinear/Native/994273.aparc.a2009s.native.dlabel.nii
Structural_preproc/MNINonLinear/Native/994273.aparc.native.dlabel.nii
Structural_preproc/MNINonLinear/Native/994273.L.aparc.a2009s.native.label.gii
Structural_preproc/MNINonLinear/Native/994273.L.aparc.native.label.gii
Structural_preproc/MNINonLinear/Native/994273.R.aparc.a2009s.native.label.gii
Structural_preproc/MNINonLinear/Native/994273.R.aparc.native.label.gii
If you get the structural extended packages, you can get the original
Freesurfer subject directory (e.g. Structural_preproc/T1w/994273).
Note these include not only the Desikan-Killiany (aparc), but also the
Destrieux (aparc.a2009s):
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
The only relation these have to the Conte69 is that they are both available in
the 164k and 32k standard meshes. These are very nice parcellations Freesurfer
provides in normal processing; we just make them available on different
meshes/formats for the HCP subjects.
I assume you are interested in anatomical parcellations only, and not
functional (e.g.,
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). I
think you will see improved parcellations coming out soon, so stay tuned.
I am not a diffusion expert, so I don't have a good feel for what you are
trying to do, though it may involve identifying where tracts terminate and
seeing how often varying parcellations agree using the same tracts (???).
Donna
On Nov 13, 2015, at 8:35 AM, Matthew George Liptrot <matthew.lipt...@di.ku.dk>
wrote:
> Hiya,
>
> We would like to compare several parcellation schemes with the results of
> structural connectivity on the HCP data (we have generated dense connectome
> data for several subjects).
> The Freesurfer parcellation (which is based upon the Conte69 atlas?) is
> already provided on the 32K subject mesh, but we would like to compare
> others, e.g. Desikan-Killiany, Harvard-Oxford, microstructure etc. In short:
>
> 1) What would be the optimal way to do this?
> 2) Which wb_commands should we use?
> 3) Which atlases would people recommend (we want to look at replication
> performance across subjects)
> 4) There seems to only be a small subset of Brodmann areas in the distributed
> subjects’ 32K CIFTI files (mainly the visual cortex and areas around pre- and
> post-central gyrus). Any reason why the rest are missing?
>
> Thanks in advance for any pointers!
>
> Cheers,
>
> M@
>
> On 4/11/15 23:17 , "Jennifer Elam" <el...@pcg.wustl.edu> wrote:
>
> Hi Vishal,
> Also, the FreeSurfer-generated aparc and aparc.a2009s non-overlapping
> parcellations for each subject are available on the 32k_fs_LR mesh and 164k
> mesh in the Structural preprocessed package for each subject. These are
> available as GIFTI label files per hemisphere and as CIFTI dlabel files (both
> hemispheres).
>
> Best,
> Jenn
>
> Jennifer Elam, Ph.D.
> Outreach Coordinator, Human Connectome Project
> Washington University School of Medicine
> Department of Anatomy and Neurobiology, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> el...@pcg.wustl.edu
> www.humanconnectome.org
>
> From: hcp-users-boun...@humanconnectome.org
> [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Harms, Michael
> Sent: Wednesday, November 04, 2015 3:40 PM
> To: Vishal Patel; hcp-users@humanconnectome.org
> Subject: Re: [HCP-Users] Hcp Data with non-overlapping parcellations
>
>
> Hi Vishal,
> There is a version of the hard parcellation from Gordon et al. (Cerebral
> Cortex, 2014) available as a CIFTI 'dlabel.nii' file, if you are interested
> in that.
>
> 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: Vishal Patel <vpatel1...@gmail.com>
> Date: Wednesday, November 4, 2015 1:42 PM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Hcp Data with non-overlapping parcellations
>
> Hi,
>
> Does anyone have access to HCP data that has been parcellated in
> non-overlapping regions or can point me in the right direction?
>
> Thanks,
>
> Vishal
>
>
>
> --
> Vishal Patel
> Graduate Student
> Applied Cognition & Neuroscience
> University of Texas at Dallas
>
> In the depths of winter, I finally learned that within me there lay an
> invincible summer.
> -Albert Camus-
>
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> --
> Matthew George Liptrot
>
> Department of Computer Science
> University of Copenhagen
> &
> Section for Cognitive Systems
> Department of Applied Mathematics and Computer Science
> Technical University of Denmark
>
> http://about.me/matthewliptrot
>
>
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