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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)

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.

Platform topics

LinuxBoxUbuntuMint2013Report

Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution.

Scripts

QaImageScripts

Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA

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.

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

Issues

gwissue_labeledit

Issues regarding the tksurfer functionality relating to creating and editing labels and annotations

Wiki

WikiInsertImage

Distilled instructions on how to insert an image on a wiki page

Test Pages

Reference Pages

GrahamWideman (last edited 2013-10-10 03:40:06 by GrahamWideman)