Differences between revisions 35 and 59 (spanning 24 versions)

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

SystemInfo

-  ⇤ ← Revision 35 as of 2008-01-22 02:07:33 → 
  Size: 1382
  Editor: GrahamWideman
  Comment:
+   ← Revision 59 as of 2013-06-26 19:27:12 → ⇥
  Size: 2829
  Editor: GrahamWideman
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-||'''Link'''||'''Description'''||
+||<#D0D0D0>'''Link'''||<#D0D0D0>'''Description'''||
|| || ||
||<-2#D0D0D0>'''Concepts''' (articles by me)||
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-||<^>LabelsClutsAnnotationFiles||Article on labels, colortables and annotations ||
||<^>RegTemplateParcAtlas ||Overview: [[BR]] --Creating and using "tif" templates for spherical registration of surfaces[[BR]] --Creating and using GCA atlas files for parcellation||
||<^>...RegTemplateParcAtlas/TemplateCreate||Creating a template for spherical registration (mris_make_template)||
||<^>...RegTemplateParcAtlas/TemplateUse||Using a template (mris_register)||
||<^>...RegTemplateParcAtlas/AtlasCreate||Creating an atlas for parcellation (mris_ca_train) ||
||<^>...RegTemplateParcAtlas/AtlasUse||Parcellation by applying an atlas (mris_ca_label)||
||<^> || ||
||<^>QaImageScripts||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA ||
+||<^>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.||
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-||'''Commands'''||(... for which I wrote some documentation) ||
||["mris_curvature_stats"] || ||
||["mris_label2annot"] || ||
||["mri_annotation2label"]|| ||
||["mris_make_template"]|| ||
||["mri_make_template"]|| ||
+||<-2#D0D0D0>'''Platform topics'''||
||<^>[[LinuxBoxUbuntuMint2013Report]]||Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution. ||
|| || ||
||<-2#D0D0D0>'''Scripts'''||
||<^>[[QaImageScripts]]||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA ||
|| || ||
||<-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.||
|| || ||
||<-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||
|| || ||
|| || ||
||<-2#D0D0D0>'''Issues'''||
||<^>[[gwissue_labeledit]]||Issues regarding the tksurfer functionality relating to creating and editing labels and annotations||
|| || ||
||<-2#D0D0D0>'''Wiki'''||
||<^>WikiInsertImage||Distilled instructions on how to insert an image on a wiki page||
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+== Reference Pages ==
 * [[SystemInfo]]