Yep, exactly! Thanks for translating my technobabble, Matt! :-) Cheers
M@ Sent from my iPhone On 18 Sep 2015, at 15:08, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: He undoubtably means the difference between FreeSurfer registration (used to generate the individual subject labels) and MSMSulc registration used to align subjects in the HCP. Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>> Date: Friday, September 18, 2015 at 8:05 AM To: Matthew George Liptrot <[email protected]<mailto:[email protected]>>, HCP Listserv <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Mapping grayordinate vertices to atlas labels Hi Matthew, Not sure if I follow the latter part of your statement. There is no "parcel alignment" process. The labeling from the Desikan-Killiany atlas on the FS native mesh is simply transferred to the 164k_fs_LR mesh and down sampled to the 32k_fs_LR mesh. 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: [email protected]<mailto:[email protected]> From: Matthew George Liptrot <[email protected]<mailto:[email protected]>> Date: Friday, September 18, 2015 6:18 AM To: HCP Listserv <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Mapping grayordinate vertices to atlas labels Doh, of course, sorry – stupid mistake: I forgot that the Desikan–Killiany atlas is adaptive to each subject. And the metric used for parcel alignment will show some differences to the metric used to align the HCP vertices, hence a variable parcel:vertex mapping will occur, right? Thanks for the clarification, M@ On 16/9/15 16:10 , "Harms, Michael" <[email protected]<mailto:[email protected]>> wrote: 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: [email protected]<mailto:[email protected]> From: Matthew George Liptrot <[email protected]<mailto:[email protected]>> Date: Wednesday, September 16, 2015 9:02 AM To: HCP Listserv <[email protected]<mailto:[email protected]>> 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 <http://about.me/matthewliptrot> 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 <http://about.me/matthewliptrot> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]> 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
