Differences between revisions 1 and 6 (spanning 5 versions)

Overview

Original description: mrisp_paint - Paints a parameterization onto a surface and outputs the results as a curvature file.

Ie: Extracts a variable (an array) from a template file, and resamples it to a given surface's vertices, outputting the result in a curvature-format (one-value-per-vertex) file.

Synopsis

mrisp_paint [options] <template 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 parameter, typically 3 as in the standard template. To select a particular parameter, 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. This selects from the template the second frame of the selected parameter, and invokes some other computations.
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

The output is a file containing a surface-worth of per-vertex values, saved in "curvature" format. The per-vertex values are the selected variable from the template file, sampled to the given surface.

Description

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.

Notes

1. I (GW) am fairly certain that it only makes sense to use a sphere as the input surface to which to resample the template data. At that, it probably only produces a useful result to resample the data to the ?h.sphere.reg file of a subject that's been registered to this template. (Of course, once that's done, the output curv-format file can be displayed on any of the same subject's surfaces.)

2. The ?h.sphere (and ?h.sphere.reg) of subject fsaverage is an evenly-gridded icosahedron which would make a particularly regular surface to use with mris_paint, if the objective is simply to visualize a template variable. (I think).

Examples

Example 1

Command:

description

Bugs

None

Links

FreeSurfer, FsFast

Methods Description

N/A

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Document Author(s)

DougGreve, BruceFischl, GrahamWideman

-  ⇤ ← Revision 1 as of 2004-09-13 11:13:29 → 
  Size: 1806
  Editor: JorgeJovicich
  Comment:
+   ← Revision 6 as of 2008-01-24 09:05:55 → ⇥
  Size: 4502
  Editor: GrahamWideman
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 12:
+= Overview =
Original description: mrisp_paint - Paints a parameterization onto a surface and outputs the results as a curvature file.
-Line 13:
+Line 15:
-= Name =
mrisp_paint -  Paints a parameterization onto a surface and outputs
the results as a curvature file.
+Ie: Extracts a variable (an array) from a template file, and resamples it to a given surface's vertices, outputting the result in a curvature-format (one-value-per-vertex) file.
 Line 18:
-mrisp_paint [options] <parameterization file> <input surface> <output name>
+mrisp_paint [options] <template file> <input surface> <output name>
 Line 22:
-|| 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 parameter, typically 3 as in the standard template. To select a particular parameter, 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||
-Line 27:
+Line 28:
-|| -flag1 ?? || brief description || detailed description (eg, help file information) ||
|| -flag2 ?? || brief description || detailed description (eg, help file information) ||
+none
 Line 31:
-|| -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. This selects from the template the second frame of the selected parameter, and invokes some other computations.||
||<^>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||<^> ||<^>||
-Line 35:
+Line 46:
-|| ?? || description ||
|| ?? || description ||
+The output is a file containing a surface-worth of per-vertex values, saved in "curvature" format. The per-vertex values are the selected variable from the template file, sampled to the given surface.
-Line 39:
+Line 49:
-This program paints a parameterization onto a surface and outputs the results as a curvature file.
+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.

= Notes =
1. I (GW) am fairly certain that it only makes sense to use a sphere as the input surface to which to resample the template data. At that, it probably only produces a useful result to resample the data to the ?h.sphere.reg file of a subject that's been registered to this template. (Of course, once that's done, the output curv-format file can be displayed on any of the same subject's surfaces.)

2. The ?h.sphere (and ?h.sphere.reg) of subject fsaverage is an evenly-gridded icosahedron which would make a particularly regular surface to use with mris_paint, if the objective is simply to visualize a template variable.  (I think).
-Line 43:
+Line 61:
-Command:

description

== Example 2 ==
-Line 56:
+Line 69:
-["othercommand1"], ["othercommand2"]
+["mris_make_template"], TemplateTifImageFiles
-Line 72:
+Line 85:
-= Author/s =
DougGreve, BruceFischl
+= Document Author(s) =
DougGreve, BruceFischl, GrahamWideman