So, cifti is not a 1:1 mapping to surface vertices. If what you plan to use can read gifti, the less error-prone route is probably to use -cifti-separate to get a nifti volume and gifti files that do have a 1:1 mapping to vertices.
Otherwise, have a look at -cifti-label-export-table, -cifti-convert -to-text (other options exist here for nifti-1 and gifti), and -cifti-export-dense-mapping in order to get text files that can get you to the vertex mapping. Tim On Tue, Nov 17, 2015 at 11:25 AM, <[email protected]> wrote: > 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 wasn’t very clear > > on explaining what we are trying to achieve – I’ll 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 FSL’s 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 > > individual’s 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 -file–information > > > 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)? > > > > I’m 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 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" > > <[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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
