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||<#D0D0D0>'''Link'''||<#D0D0D0>'''Description'''|| |
||<#D0D0D0>'''Link''' ||<#D0D0D0>'''Description''' || |
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||<-2#D0D0D0>'''Concepts''' (articles by me)|| ||<^>ReconAllFilesVsSteps||Cross-reference table showing files read and written by each step in recon-all|| ||<^>LabelsClutsAnnotationFiles||Article on '''labels''', '''colortables''' and '''annotations''' || ||<^>[[tksurfer_labeledit]] ||'''Editing labels/annotations''' in tksurfer|| ||<^>SurfaceRegAndTemplates ||Creating and using '''"tif" templates''' for spherical registration of surfaces|| ||<^>SurfaceLabelAtlas ||Creating and using '''GCA atlas files''' for parcellation|| ||<^>TemplateTifImageFiles||Discussion of the contents and format of the so-called "Image" file format used to store !FreeSurfer surface-registration template data.|| |
||||<#D0D0D0>'''Concepts''' (articles by me) || ||<style="vertical-align:top">ReconAllFilesVsSteps ||Cross-reference table showing files read and written by each step in recon-all || ||<style="vertical-align:top">LabelsClutsAnnotationFiles ||Article on '''labels''', '''colortables''' and '''annotations''' || ||<style="vertical-align:top">[[tksurfer_labeledit]] ||'''Editing labels/annotations''' in tksurfer || ||<style="vertical-align:top">SurfaceRegAndTemplates ||Creating and using '''"tif" templates''' for spherical registration of surfaces || ||<style="vertical-align:top">SurfaceLabelAtlas ||Creating and using '''GCA atlas files''' for parcellation || ||<style="vertical-align:top">TemplateTifImageFiles ||Discussion of the contents and format of the so-called "Image" file format used to store !FreeSurfer surface-registration template data. || |
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||<-2#D0D0D0>'''Platform topics'''|| ||<^>[[LinuxBoxUbuntuMint2013Report]]||Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution. || |
||||<#D0D0D0>'''Platform topics''' || ||<style="vertical-align:top">LinuxBoxUbuntuMint2013Report ||Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution. || |
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||<-2#D0D0D0>'''Scripts'''|| ||<^>[[QaImageScripts]]||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA || |
||||<#D0D0D0>'''Scripts''' || ||<style="vertical-align:top">QaImageScripts ||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA || |
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||<-2#D0D0D0>'''Programs/Scripts''' (... for which I wrote some documentation) || ||<^>[[tksurfer]] ||Freesurfer's surface-viewing application. (I completed the list of flagged arguments.)|| ||<^>[[mris_curvature_stats]] ||Curvature-related statistics || ||<^>[[mris_label2annot]] ||Combine label files plus colortable into an annotation file || ||<^>[[mri_annotation2label]]||Extract label file from annotation file || ||<^>[[mris_make_template]]||Use data from multiple subjects to create a surface registration template file || ||<^>[[mri_make_template]]||Use data from multiple subjects to create a volume registration template || ||<^>[[mris_register]]||For one subject, register to a registration template (usually resulting in ?h.sphere.reg) || ||<^>[[mrisp_paint]]||"Paint" data from a template file "onto a given surface". Allows viewing data from a template file.|| |
||||<#D0D0D0>'''Programs/Scripts''' (... for which I wrote some documentation) || ||<style="vertical-align:top">[[tksurfer]] ||Freesurfer's surface-viewing application. (I completed the list of flagged arguments.) || ||<style="vertical-align:top">[[mris_curvature_stats]] ||Curvature-related statistics || ||<style="vertical-align:top">[[mris_label2annot]] ||Combine label files plus colortable into an annotation file || ||<style="vertical-align:top">[[mri_annotation2label]] ||Extract label file from annotation file || ||<style="vertical-align:top">[[mris_make_template]] ||Use data from multiple subjects to create a surface registration template file || ||<style="vertical-align:top">[[mri_make_template]] ||Use data from multiple subjects to create a volume registration template || ||<style="vertical-align:top">[[mris_register]] ||For one subject, register to a registration template (usually resulting in ?h.sphere.reg) || ||<style="vertical-align:top">[[mrisp_paint]] ||"Paint" data from a template file "onto a given surface". Allows viewing data from a template file. || |
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||<-2#D0D0D0>'''Source code suggestions'''|| ||<^>[[gwcode_tksurfer_delink]]||Code relating to -delink|| ||<^>[[gwcode_tksurfer_labelresize]]||Code to allow the tool window's per-vertex data fields to expand on window resize|| |
||||<#D0D0D0>'''Source code suggestions''' || ||<style="vertical-align:top">[[gwcode_tksurfer_delink]] ||Code relating to -delink || ||<style="vertical-align:top">[[gwcode_tksurfer_labelresize]] ||Code to allow the tool window's per-vertex data fields to expand on window resize || |
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||<-2#D0D0D0>'''Issues'''|| ||<^>[[gwissue_labeledit]]||Issues regarding the tksurfer functionality relating to creating and editing labels and annotations|| |
||||<#D0D0D0>'''Issues''' || ||<style="vertical-align:top">[[gwissue_labeledit]] ||Issues regarding the tksurfer functionality relating to creating and editing labels and annotations || |
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||<-2#D0D0D0>'''Wiki'''|| ||<^>WikiInsertImage||Distilled instructions on how to insert an image on a wiki page|| |
||||<#D0D0D0>'''Wiki''' || ||<style="vertical-align:top">WikiInsertImage ||Distilled instructions on how to insert an image on a wiki page || |
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* [[SystemInfo]] * [[WikiConfig]] * [[WikiConfigHelp]] |
* SystemInfo * WikiConfig * WikiConfigHelp * GrahamWidemanTimeStamp |
GrahamWideman pages
Useful pages
Link |
Description |
|
|
Concepts (articles by me) |
|
Cross-reference table showing files read and written by each step in recon-all |
|
Article on labels, colortables and annotations |
|
Editing labels/annotations in tksurfer |
|
Creating and using "tif" templates for spherical registration of surfaces |
|
Creating and using GCA atlas files for parcellation |
|
Discussion of the contents and format of the so-called "Image" file format used to store FreeSurfer surface-registration template data. |
|
|
|
Platform topics |
|
Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution. |
|
|
|
Scripts |
|
Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA |
|
|
|
Programs/Scripts (... for which I wrote some documentation) |
|
Freesurfer's surface-viewing application. (I completed the list of flagged arguments.) |
|
Curvature-related statistics |
|
Combine label files plus colortable into an annotation file |
|
Extract label file from annotation file |
|
Use data from multiple subjects to create a surface registration template file |
|
Use data from multiple subjects to create a volume registration template |
|
For one subject, register to a registration template (usually resulting in ?h.sphere.reg) |
|
"Paint" data from a template file "onto a given surface". Allows viewing data from a template file. |
|
|
|
Source code suggestions |
|
Code relating to -delink |
|
Code to allow the tool window's per-vertex data fields to expand on window resize |
|
|
|
|
|
Issues |
|
Issues regarding the tksurfer functionality relating to creating and editing labels and annotations |
|
|
|
Wiki |
|
Distilled instructions on how to insert an image on a wiki page |
|
|
|
Test Pages
GrahamWideman