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| Describe GrahamWideman here. | = GrahamWideman pages = |
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| Just a test. | == Useful pages == |
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| Emphasis: ''italics''; '''bold'''; '''''bold italics'''''; ''mixed '''bold''' and italics''; ---- horizontal rule. Headings: = Title 1 =; == Title 2 ==; === Title 3 ===; ==== Title 4 ====; ===== Title 5 =====. Lists: space and one of * bullets; 1., a., A., i., I. numbered items; 1.#n start numbering at n; space alone indents. Links: JoinCapitalizedWords; ["brackets and double quotes"]; url; [url]; [url label]. Tables: || cell text |||| cell text spanning two columns ||; no trailing white space allowed after tables or titles. ---- CategoryCategory |
||<#D0D0D0>'''Link'''||<#D0D0D0>'''Description'''|| || || || ||<-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.|| || || || ||<-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|| || || || == Test Pages == * GrahamWideman * GrahamWideman/MoinEditorBackup * GrahamWidemanTest01 * GrahamWidemanTest02 * GrahamWidemanTest03 * GrWiAccessControlTest * GrWiTestNewPage == Reference Pages == * [[SystemInfo]] * [[WikiConfigHelp]] |
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