-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
Tim
On Wed, Sep 10, 2014 at 10:36 AM, Glasser, Matthew <[email protected]>
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" <[email protected]> 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" <[email protected]> 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
> >>> _______________________________________________
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> >>> [email protected]
> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >>
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