Try this: wb_command -gifti-convert ASCII my.label.gii ascii.label.gii
If needed, strip everything up to <Data>, and then the label values are listed in vertex sequence. Will need to think about the HOA question. Hmmm. Donna > Hi Donna, > > Many thanks for your thorough reply. I can see that I wasnât very clear > on explaining what we are trying to achieve â Iâll try to clarify > things a little :-) > > What we have done so far: > Generated Conn3.dconn.nii files: 92K x 92K structural connectivity > matrices from the DWI data in FSLâs matrix3 format (WM seeds, cortical > surface & subcortical voxels as targets). > This provides us with connectivity matrices whose nodes are (to the limit > of the HCP registration pipeline) anatomically matched across subjects. > > What we are analyzing: > Machine-learning parcellation of these connectivity matrices. > > What we would like to do: > Compare our machine-learning parcellations with previously published / > commonly-used ones. > For this we would like to be able to obtain, for each atlas, a label per > node of the connectivity matrices. > For some atlases, e.g. Desikan-Killiany, I realise that these labels:node > mappings will vary per subject as the atlas is adapted according to the > individualâs gyrification patterns. > For other atlases though, e.g. the Gordon 2014 atlas, the label:node > mapping is fixed. > It would also be great if we could compare against some MNI-based > parcellation schemes, such as the Harvard-Oxford. (Other suggestions > welcome!) > > So to my questions! :-) > > 1) What is the best way to get the per-subject label:node mapping from the > existing *.dlabel.nii and *.label.gii files? > I was thinking of using something like: > > wb_command -fileâinformation > 100307/MNINonLinear/fsaverage_LR32k/100307.aparc.a2009s.32k_fs_LR.dlabel.nii > > which gives me (with a bit of filtering) a parcel:label mapping. > Then using: > > wb_command -nifti-information -print-matrix > 100307/MNINonLinear/fsaverage_LR32k/100307.aparc.a2009s.32k_fs_LR.dlabel.nii > > to give me a vertex:parcel mapping. Then I need to stitch the two together > somehow. > Are these steps correct? Is there a better (easier) way? > > 2) Would I use the same method for the Gordon atlas (which I understand is > provided on the standard 32K mesh)? > > 3) How would I do this for, e.g. the Harvard-Oxford atlas? Should I map > the voxelwise parcels onto the 32K mesh first and then use the same method > as for (2)? > > Iâm still a surface-space novice, but I hope this is a bit clearer now > :-) > > Many thanks for any help/advice! > > Cheers, > > M@ > > On 13/11/15 20:25 , "Donna Dierker" > <[email protected]<mailto:[email protected]>> wrote: > > 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 > <[email protected]<mailto:[email protected]>> 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 subjectsâ 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" > <[email protected]<mailto:[email protected]>> 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 > [email protected]<mailto:[email protected]> > www.humanconnectome.org > > From: > [email protected]<mailto:[email protected]> > [mailto:[email protected]] On Behalf Of Harms, > Michael > Sent: Wednesday, November 04, 2015 3:40 PM > To: Vishal Patel; > [email protected]<mailto:[email protected]> > 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: [email protected]<mailto:[email protected]> > > From: Vishal Patel <[email protected]<mailto:[email protected]>> > Date: Wednesday, November 4, 2015 1:42 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > 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- > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the > contents of this information is strictly prohibited. If you have received > this email in error, please immediately notify the sender via telephone or > return mail. > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -- > 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 > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > -- > Matthew George Liptrot > > <http://about.me/matthewliptrot> > 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 > > <http://about.me/matthewliptrot> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
