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| = Name = mrisp_paint - Paints a parameterization onto a surface and outputs the results as a curvature file. |
= Overview = Original description: mrisp_paint - Paints a parameterization onto a surface and outputs the results as a curvature file. Explanation: This program is useful for extracting one of the arrays ("a variable") from a surface-registration template file. The output is a file containing a surface-worth of per-vertex values, saved in "curvature" format. Because the template data is sampled to a particular surface mesh, this conjures the idea of "painting to a surface". For more information on surface-registration template files, see TemplateTifImageFiles. |
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| || parametrization file || Specify parametrization file name || What is this? || || input surface || Specify input surface name || || || ouput name || Specify output curvature file || || |
||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''|| ||<^>1||<^> <template_fname> ||<^>Full path to template_file. Template file is usually a tif file (not a picture image; tif format is just used to contain !FreeSurfer array data). Template may contain more than one array, called a 'frame' in FS lingo, typically 9 frames (3 x 3) as in the standard template. To select a particular frame, append '#' followed by frame number. Eg: 'somepath/mytemplate.tif#1'. Numbering starts at 0, which is the default.|| ||<^>2||<^> <surf_fname> ||<^>Full path to surface file which will provide the grid (vertices) onto which the template data is to be sampled or 'painted'. (See note below on what kind of surface is suitable.)|| ||<^>3||<^> <out_fname> ||<^>Output file name. Can be full path, or if directory omitted then will save to same directory as surf_fname|| |
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| || -flag1 ?? || brief description || detailed description (eg, help file information) || || -flag2 ?? || brief description || detailed description (eg, help file information) || |
none |
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| || -flag3 ??|| brief description ||detailed description (eg, help file information) || || -flag4 ??|| brief description ||detailed description (eg, help file information) || |
||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''|| ||<^>Input||<^>-SDIR||<^> <subjects_dir> ||<^>Set SUBJECTS_DIR. Default: use environment variable/|| ||<^>Algorithm||<^>-A||<^> <navgs> ||<^>Average curvature patterns navgs times|| ||<^>Algorithm||<^>-N||<^> ||<^>Normalize curvature by variance.|| ||<^>Algorithm||<^>-S||<^> ||<^>Take square-root of output variable|| ||<^>Algorithm||<^>-variance||<^> <subject_name hemi field_no> ||<^>Generate variance map|| ||<^>Utility||<^>-?,-U||<^> ||<^>Print usage|| ||<^>Utility||<^>--all-info, -all-info||<^> ||<^>Prints BIRN-standard program information|| ||<^>Utility||<^>--help||<^> ||<^>Prints help message|| ||<^>Utility||<^>-V||<^> <vertex_num (int)> ||<^>Invoke diagnostics for vertex number vertex_num|| ||<^>Utility||<^>--version, -version||<^> ||<^>Prints version information|| ||<^>Utility||<^>-W||<^> ||<^>Write some diagnostics (DIAG_WRITE)|| ||<^>Footer||<^>XXXXXXXXXXXXX||<^> ||<^>|| |
Index TableOfContents
Overview
Original description: mrisp_paint - Paints a parameterization onto a surface and outputs the results as a curvature file.
Explanation: This program is useful for extracting one of the arrays ("a variable") from a surface-registration template file. The output is a file containing a surface-worth of per-vertex values, saved in "curvature" format. Because the template data is sampled to a particular surface mesh, this conjures the idea of "painting to a surface".
For more information on surface-registration template files, see TemplateTifImageFiles.
Synopsis
mrisp_paint [options] <parameterization file> <input surface> <output name>
Arguments
Positional Arguments
Posn |
<Argname> |
Description |
1 |
<template_fname> |
Full path to template_file. Template file is usually a tif file (not a picture image; tif format is just used to contain FreeSurfer array data). Template may contain more than one array, called a 'frame' in FS lingo, typically 9 frames (3 x 3) as in the standard template. To select a particular frame, append '#' followed by frame number. Eg: 'somepath/mytemplate.tif#1'. Numbering starts at 0, which is the default. |
2 |
<surf_fname> |
Full path to surface file which will provide the grid (vertices) onto which the template data is to be sampled or 'painted'. (See note below on what kind of surface is suitable.) |
3 |
<out_fname> |
Output file name. Can be full path, or if directory omitted then will save to same directory as surf_fname |
Required Flagged Arguments
none
Optional Flagged Arguments
Category |
Flag |
<Args> |
Description |
Input |
-SDIR |
<subjects_dir> |
Set SUBJECTS_DIR. Default: use environment variable/ |
Algorithm |
-A |
<navgs> |
Average curvature patterns navgs times |
Algorithm |
-N |
|
Normalize curvature by variance. |
Algorithm |
-S |
|
Take square-root of output variable |
Algorithm |
-variance |
<subject_name hemi field_no> |
Generate variance map |
Utility |
-?,-U |
|
Print usage |
Utility |
--all-info, -all-info |
|
Prints BIRN-standard program information |
Utility |
--help |
|
Prints help message |
Utility |
-V |
<vertex_num (int)> |
Invoke diagnostics for vertex number vertex_num |
Utility |
--version, -version |
|
Prints version information |
Utility |
-W |
|
Write some diagnostics (DIAG_WRITE) |
Footer |
XXXXXXXXXXXXX |
|
Outputs
?? |
description |
?? |
description |
Description
This program paints a parameterization onto a surface and outputs the results as a curvature file.
Examples
Example 1
Command:
description
Example 2
Command:
description
Bugs
None
See Also
["othercommand1"], ["othercommand2"]
Links
Methods Description
N/A
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>