Re: [HCP-Users] Mapping grayordinate vertices to atlas labels

[Harms, Michael]

No, there is going to variability in the label for a given vertex across subjects.  You would want to use the aparc.a2009s.32k_fs_LR.dlabel.nii that is specific to each subject. 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: Matthew George Liptrot <matthew.lipt...@di.ku.dk> Date: Wednesday, September 16, 2015 9:02 AM To: HCP Listserv <hcp-users@humanconnectome.org> Subject: [HCP-Users] Mapping grayordinate vertices to atlas labels Hi, After generating dense connectivity maps (*.dconn.nii files) from the HCP DWI data, we would like to use previous parcellations (e.g. Desikan-Killiany) to assess the reproducibility across subjects. As the grayordinates vertices are assumed to be anatomically-matched across subjects, then there should be a single lookup table to convert from HCP grayordinates to a given parcellation, correct? If so, does anyone have this as a simple table? If not, what is the easiest way to generate it? I realise that I can print out a (apparently zero-based) lookup table of Label_IDs and Label_Names by doing: wb_command -file–information 100307/MNINonLinear/fsaverage_LR32k/100307.aparc.a2009s.32k_fs_LR.dlabel.nii Which produces: Name:                    100307.aparc.a2009s.32k_fs_LR.dlabel.nii Type:                    Connectivity - Dense Label Structure:               CortexLeft CortexRight  Data Size:               237.65 Kilobytes Maps to Surface:         true Maps to Volume:          false Maps with LabelTable:    true Maps with Palette:       false Number of Maps:          1 Number of Rows:          59412 Number of Columns:       1 Volume Dim[0]:           0 Volume Dim[1]:           0 Volume Dim[2]:           0 Palette Type:            None CIFTI Dim[0]:            1 CIFTI Dim[1]:            59412 ALONG_ROW map type:      LABELS ALONG_COLUMN map type:   BRAIN_MODELS     Has Volume Data:     false     CortexLeft:          29696 out of 32492 vertices     CortexRight:         29716 out of 32492 vertices Map   Map Name                 1   100307_aparc.a2009s    Label table for ALL maps        KEY   NAME                            RED   GREEN    BLUE   ALPHA             0   ???                           0.000   0.000   0.000   0.000             1   L_G_and_S_frontomargin        0.090   0.863   0.235   1.000             2   L_G_and_S_occipital_inf       0.090   0.235   0.706   1.000             3   L_G_and_S_paracentral         0.247   0.392   0.235   1.000    …        147   R_S_subparietal               0.396   0.235   0.235   1.000           148   R_S_temporal_inf              0.082   0.706   0.706   1.000           149   R_S_temporal_sup              0.875   0.863   0.235   1.000           150   R_S_temporal_transverse       0.867   0.235   0.235   1.000     Also, the following command:  wb_command -nifti-information -print-matrix 100307/MNINonLinear/fsaverage_LR32k/100307.aparc.a2009s.32k_fs_LR.dlabel.nii  produces the Label_ID : Vertex_Number mapping (again apparently zero-based): Row 0: 72 Row 1: 27 Row 2: 29 Row 3: 16 Row 4: 59 Row 5: 26 … Row 59407: 113 Row 59408: 113 Row 59409: 113 Row 59410: 113 Row 59411: 113 Is this the correct data to use to create a (label_name : vertex_number) lookup table? Cheers, M@ --  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 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