Hi all, I just re-read the latest release notes. How does one access:
- Border mode improvements including Border optimize to provide semi-automatic optimization of parcel borders based on single or multi-modal gradients Is this what I'm thinking it is? (i.e., allowing parcellation given multiple outputs from wb_command -cifti-gradient?) akin to the very coarse way Matt G. and I were trying way back when? -Alex ---------------------------------------------------------------- *Alexander Li Cohen, M.D., Ph.D.* Resident Physician Child and Adolescent Neurology E-mail: [email protected] (Medical/Science Email) E-mail: [email protected] (Lifetime Email) *Mayo Clinic* 200 First Street SW Rochester, MN 55905 mayoclinic.org ---------------------------------------------------------------- On Wed, Sep 16, 2015 at 1:00 PM, <[email protected]> wrote: > Send HCP-Users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > Today's Topics: > > 1. Mapping grayordinate vertices to atlas labels > (Matthew George Liptrot) > 2. Re: Mapping grayordinate vertices to atlas labels > (Stamatios Sotiropoulos) > 3. Re: Mapping grayordinate vertices to atlas labels (Harms, Michael) > > > ---------- Forwarded message ---------- > From: Matthew George Liptrot <[email protected]> > To: HCP Listserv <[email protected]> > Cc: > Date: Wed, 16 Sep 2015 14:02:38 +0000 > 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> > > > ---------- Forwarded message ---------- > From: Stamatios Sotiropoulos <[email protected]> > To: Matthew George Liptrot <[email protected]> > Cc: HCP Listserv <[email protected]> > Date: Wed, 16 Sep 2015 14:09:14 +0000 > Subject: Re: [HCP-Users] Mapping grayordinate vertices to atlas labels > Hi Matthew > > look at wb_command -cifti-parcellate. > > You will need to run this twice (once along ROW and another time along > COLUMN) to get a connectome parcellated along both dimensions. > > Cheers > Stam > > > On 16 Sep 2015, at 15:02, Matthew George Liptrot <[email protected]> > wrote: > > 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] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > ---------- Forwarded message ---------- > From: "Harms, Michael" <[email protected]> > To: Matthew George Liptrot <[email protected]>, HCP Listserv < > [email protected]> > Cc: > Date: Wed, 16 Sep 2015 14:10:57 +0000 > Subject: Re: [HCP-Users] Mapping grayordinate vertices to atlas labels > > 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] > > From: Matthew George Liptrot <[email protected]> > Date: Wednesday, September 16, 2015 9:02 AM > To: HCP Listserv <[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] > 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. 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