Thanks that's really helpful. Using this info I can load into matlab and with vertices in the 32k fs_LR space. The last hurdle is registering subject-space freesurfer vertices surface to the 32k fs_LR vertices, so that I can transfer the labels over to workbench. The caret wiki mentions a freesurfer to 32k pipeline - is it generally available yet?
Thanks again for all the help Konrad On 2014-09-10 23:38, Timothy Coalson wrote: > -cifti-separate is probably what you want, if you want to use spatial > and/or surface neighbor information (because the indices in the metric > files will line up with the relevant surface files). Also, with the > v1.0 release, the -file-information command will give you a quick > summary of the mappings, like so: > > ALONG_ROW map type: SCALARS > ALONG_COLUMN map type: BRAIN_MODELS > CortexLeft: 29696 out of 32492 vertices > CortexRight: 29716 out of 32492 vertices > AccumbensLeft: 135 voxels > AccumbensRight: 140 voxels > AmygdalaLeft: 315 voxels > AmygdalaRight: 332 voxels > BrainStem: 3472 voxels > CaudateLeft: 728 voxels > CaudateRight: 755 voxels > CerebellumLeft: 8709 voxels > CerebellumRight: 9144 voxels > DiencephalonVentralLeft: 706 voxels > DiencephalonVentralRight: 712 voxels > HippocampusLeft: 764 voxels > HippocampusRight: 795 voxels > PallidumLeft: 297 voxels > PallidumRight: 260 voxels > PutamenLeft: 1060 voxels > PutamenRight: 1010 voxels > ThalamusLeft: 1288 voxels > ThalamusRight: 1248 voxels > > If you need to know the details of how CIFTI indices map to surface > vertices and/or voxels, there is also this new command, which will > give text files containing the mapping information: > > http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-export-dense-mapping > [2] > > Tim > > On Wed, Sep 10, 2014 at 10:36 AM, Glasser, Matthew > <glass...@wusm.wustl.edu> wrote: > >> You can look at the header (which is XML) to see, but the typical >> order is >> left surface, right surface, and then subcortical. Also, it is not >> 32492 >> vertices for the surfaces because the medial wall is excluded. If >> for >> some reason you need to process the different components >> separately, you >> can use wb_command -cifti-separate as well. >> >> Peace, >> >> Matt. >> >> On 9/10/14, 1:59 AM, "K. Wagstyl" <kw...@cam.ac.uk> wrote: >> >>> Thanks Matt - the matlab scripts are working great. >>> Can I check the structure for grayordinate data? >>> >>> Is it the first 32492 vertices are left hemisphere surface, >>> then left subcortical, >>> then the next 32492 are right hemisphere surface, >>> then right subcortical? >>> >>> Cheers, >>> Konrad >>> >>> On 2014-09-09 20:48, Glasser, Matthew wrote: >>>> I¹d recommend option ii. >>>> >>>> You can use the surfaces and label data in the >>>> ${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k folder >>>> together >>>> with the dense timeseries data. To load the data into matlab, >> you can >>>> use >>>> these attached matlab functions together with wb_command and the >> matlab >>>> GIFTI toolbox: >>>> >>>> cii = ciftiopen(Œpath/to/file¹,¹path/to/wb_command¹); >>>> >>>> CIFTIdata = cii.cdata; >>>> >>>> >>>> Some lines of analysis code >>>> >>>> newcii = cii; >>>> >>>> newcii.cdata = AnalysisOutput; >>>> >>>> ciftisave(newcii,¹path/to/newfile¹,¹path/to/wb_command¹); >>>> >>>> Or if the data matrix is a different size from what you started >> with >>>> >>>> >> ciftisavereset(newcii,¹path/to/newfile¹,¹path/to/wb_command¹); >>>> >>>> And then you can view your result in Connectome Workbench¹s >> wb_view on >>>> the >>>> 32k standard surfaces. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> On 9/9/14, 10:22 AM, "K. Wagstyl" <kw...@cam.ac.uk> wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm trying to carry out some analysis on the preprocessed >>>>> resting-state >>>>> fMRI but running into some problems with the *.dtseries.nii >> files. >>>>> The first part of the analysis was carried out on structural >> data in >>>>> freesurfer and matlab (using labels etc) >>>>> Is there any way of converting the resting-state data into a >> format >>>>> for >>>>> similar analysis? >>>>> >>>>> In other words, either >>>>> i) mapping the time series to individuals' freesurfer-space >> vertices >>>>> or >>>>> ii) importing the grayordinate data into matlab? >>>>> >>>>> Thanks, >>>>> Konrad >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> HCP-Users@humanconnectome.org >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users [1] >>>> >>>> >>>> ________________________________ >>>> The materials in this message are private and may contain >> Protected >>>> Healthcare Information or other information of a sensitive >> nature. 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