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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 onto which the template data is to be ""painted"" (ie: resampled). (See note below on what kind of surface.)||" ||<^>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) || |
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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 onto which the template data is to be ""painted"" (ie: resampled). (See note below on what kind of surface.)||"
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>