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| ||'''Link'''||'''Description'''|| | ||<#D0D0D0>'''Link'''||<#D0D0D0>'''Description'''|| ||'''Concepts'''|| || |
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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)|| ||<^> || || |
||<^>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|| ||<^>TemplateTifImageFiles||Discussion of the contents and format of the so-called "Image" file format used to store !FreeSurfer surface-registration template data.|| || || || ||<#D0D0D0>'''Scripts'''||<#D0D0D0> || |
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||'''Commands'''||(... for which I wrote some documentation) || ||["mris_curvature_stats"] || || ||["mris_label2annot"] || || ||["mri_annotation2label"]|| || ||["mris_make_template"]|| || ||["mri_make_template"]|| || |
||<#D0D0D0>'''Commands'''||<#D0D0D0>(... for which I wrote some documentation) || ||<^>["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>'''Wiki'''||<#D0D0D0> || ||<^>WikiInsertImage||Distilled instructions on how to insert an image on a wiki page|| |
GrahamWideman pages
Useful pages
Link |
Description |
Concepts |
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Cross-reference table showing files read and written by each step in recon-all |
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Article on labels, colortables and annotations |
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Overview: BR --Creating and using "tif" templates for spherical registration of surfacesBR --Creating and using GCA atlas files for parcellation |
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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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Scripts |
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Sample scripts to produce "screencaps" en masse from tksurfer and tkmedit for QA |
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Commands |
(... for which I wrote some documentation) |
["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. |
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Wiki |
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Distilled instructions on how to insert an image on a wiki page |
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