Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate

[Harms, Michael]

If you are willing to use 'matlab', another option is to load the dlabel.nii into matlab, and then using the FIND command you can easily get a list of all the indices corresponding to a given (numeric) label ID. 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: mha...@wustl.edu From: Timothy Coalson <tsc...@mst.edu> Date: Tuesday, January 6, 2015 3:57 PM To: Oscar Miranda Dominguez <miran...@ohsu.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate In the dlabel.nii file, this information is in the data matrix, not the header.  One way to get this information is from the header of a ptseries.nii file (or other parcellated file type) resulting from parcellating with it.  The -file-information command should report the counts of vertices ("nodes" which is terminology we used to use, next release this will say vertices) and voxels within each parcel, like so: ... ALONG_COLUMN map type:    PARCELS     Has Volume Data:      false     CortexLeft:           32492 nodes     L_V1_ROI:             Voxel-Count=0                           CortexLeft Node-Count=679     L_MSTv_ROI:           Voxel-Count=0                           CortexLeft Node-Count=40     L_V6_ROI:             Voxel-Count=0                           CortexLeft Node-Count=122     L_V2_ROI:             Voxel-Count=0                           CortexLeft Node-Count=731     L_V3_ROI:             Voxel-Count=0                           CortexLeft Node-Count=492 ... In the Cifti XML (again, of the parcellated file, not the dlabel.nii), the lists you are looking for look like this:         <MatrixIndicesMap AppliesToMatrixDimension="1" IndicesMapToDataType="CIFTI_INDEX_TYPE_PARCELS">             <Surface BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT" SurfaceNumberOfVertices="32492"/>             <Parcel Name="L_V1_ROI">                 <Vertices BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT">100 101 102 103 104 105 106 107 108 109 1489 1510 1530 1531 1549 1550 1567 1568 1569 1584 1585 1586 1600 1601 1615 23155 23156 23157 23158 23159 23160 23161 23162 23163 23164 23165 23166 23167 23168 23169 23170 23171 23172... There are some other ways to get the information (getting the dlabel.nii data and translating indices by the brain models map), but I think this is the closest to what you are asking without using additional tools. Tim On Tue, Jan 6, 2015 at 11:29 AM, Oscar Miranda Dominguez <miran...@ohsu.edu> wrote: Hi   I need some help with an easy issue! I have a few parcellations that I am using to make timecourses using cifti-parcellate. However I am interested in knowing either of the following 2 thinks:   1.       Which grayordinate belongs to each ROI, or 2.       How many grayordinates belong to each ROI   I know that this info should be in the label file. However, when I read the header, I just see the list of ROIs and the ~32k grayordinates that belong to each hemisphere. Any suggestions?   Thanks in advance for your help and best regards!   Oscar Miranda-Dominguez Postdoctoral Researcher Fair Neuroimaging Lab Phone: 503.418.1894  Fax: 503.494.9988   Oregon Health and Science University Department of Behavioral Neuroscience 3181 SW Sam Jackson Park Road, L470 Portland, OR  97239 http://www.ohsu.edu/fair-lab   _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users