GrahamWideman pages

Link

Description

Concepts

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.

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