Those pieces of information reside in separate files. The mapping of what
area each vertex/voxel belongs to exists in the data of this cifti dlabel
file:
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.aparc.a2009s.32k_fs_LR.dlabel.nii
The various fMRI timeseries are in cifti dtseries files, under the
${StudyFolder}/${Subject}/MNINonLinear/Results directory.
The surface coordinates are in the gifti surface files, which exist here:
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.midthickness.32k_fs_LR.surf.gii
The voxel indices have to be transformed into millimeters by use of the
volume space encoded in the XML of the cifti file, but this should be the
same as the MNI 2mm volume space, which you can get from this nifti-1
volume file, if nothing else:
${StudyFolder}/${Subject}/MNINonLinear/T1w_restore.2.nii.gz
Getting the data into whatever tool you plan to use depends on what formats
it supports. For matlab, there is some code available to read cifti files,
and with the code derived from FieldTrip, information about the vertex or
voxel for each index, and the mapping between dlabel data value and area
name, should be available in the struct that the reading functions return.
See this FAQ entry:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
You will also need the matlab gifti toolbox, for the surface files:
http://www.artefact.tk/software/matlab/gifti/
If you are not using matlab, then you must have support for gifti files for
surface coordinates, and support for gifti or nifti-1 for data from cifti
files (via the -cifti-convert command). If you don't have support for
either of these, we are adding support for converting cifti data to text
files.
If you don't use the FieldTrip-derived code (or use something other than
matlab), you can get the dlabel file's mapping between label name and
integer value as a text file by using -cifti-label-export-table:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-label-export-table
Similarly, you can get the mapping between cifti indices and
vertices/voxels as text files with the -cifti-export-dense-mapping command,
by running it on the dlabel or dtseries files:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-export-dense-mapping
Tim
On Wed, Feb 11, 2015 at 10:09 PM, Peka Savayan <savay...@umn.edu> wrote:
> Hi experts,
>
>
> How do I get the list of all grayordinates, together with their unaveraged
> time series, that belong to each ROI of all cortical and subcortical areas
> of the FreeSurfer aparc.a2009s atlas? Ideally, the grayordinates would have
> their relative location and/or their coordinates.
>
>
> Can you give me details of the steps along with the commands? I am an
> absolute beginner.
>
>
> I appreciate your help.
>
> Best wishes,
>
> Peka
>
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
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