|
Size: 2491
Comment:
|
← Revision 64 as of 2013-10-10 03:40:06 ⇥
Size: 3627
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| Line 4: | Line 3: |
||<#D0D0D0>'''Link'''||<#D0D0D0>'''Description'''|| |
||<#D0D0D0>'''Link''' ||<#D0D0D0>'''Description''' || |
| Line 7: | Line 5: |
| ||<-2#D0D0D0>'''Concepts'''|| ||<^>ReconAllFilesVsSteps||Cross-reference table showing files read and written by each step in recon-all|| ||<^>LabelsClutsAnnotationFiles||Article on '''labels''', '''colortables''' and '''annotations''' || ||<^>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 style="text-align:center">'''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. || |
| Line 14: | Line 13: |
| ||<-2#D0D0D0>'''Scripts'''|| ||<^>QaImageScripts||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA || |
||||<#D0D0D0 style="text-align:center">'''Platform topics''' || ||<style="vertical-align:top">LinuxBoxUbuntuMint2013Report ||Report on configuring 2013-era desktop hardware for Linux and FreeSurfer, using Mint 15 distribution. || |
| Line 17: | Line 16: |
| ||<-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 style="text-align:center">'''Scripts''' || ||<style="vertical-align:top">QaImageScripts ||Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA || |
| Line 27: | Line 19: |
| ||<-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 style="text-align:center">'''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. || || || || ||||<#D0D0D0 style="text-align:center">'''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 || |
| Line 32: | Line 34: |
| ||<-2#D0D0D0>'''Issues'''|| ||<^>["gwissue_labeledit"]||Issues regarding the tksurfer functionality relating to creating and editing labels and annotations|| |
||||<#D0D0D0 style="text-align:center">'''Issues''' || ||<style="vertical-align:top">[[gwissue_labeledit]] ||Issues regarding the tksurfer functionality relating to creating and editing labels and annotations || |
| Line 35: | Line 37: |
| ||<-2#D0D0D0>'''Wiki'''|| ||<^>WikiInsertImage||Distilled instructions on how to insert an image on a wiki page|| |
||||<#D0D0D0 style="text-align:center">'''Wiki''' || ||<style="vertical-align:top">WikiInsertImage ||Distilled instructions on how to insert an image on a wiki page || |
| Line 39: | Line 41: |
| Line 40: | Line 43: |
| Line 45: | Line 47: |
| * GrahamWidemanTest03 | |
| Line 47: | Line 50: |
| * TitleIndexPage == Reference Pages == * 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