Index
Contents
Software version described:
- $Date: 2007/02/13 12:20:16 $
- $Revision: 1.23 $
- Use usage or version option to see version you are using
Name
mris_make_template
Overview
This program reads surface and curvature data from multiple subjects and produces a "template". This template is later used by mris_register to register the sphere surface of individual subjects to the average surface.
Related concepts are discussed here: SurfaceRegAndTemplates.
"Atlas" vs "Template": Descriptions below sometimes refer to "atlas", following the usage in this program's source code and some of its messages. However, the file produced by this program is normally referred to as a "template" file, as distinct from "atlas" which is generally used for the GCA files that capture reference maps of regions. (See also mris_ca_train.)
Synopsis
mri_make_template [Flagged args] hemi sphere_name subject1 [subject2 ...] template_name
Arguments
Positional Arguments
Posn |
<Argname> |
Description |
1 |
<hemi> |
lh or rh |
2 |
<sphere_name> |
Name of sphere surface to read from each subject. Actual filepath will be: |
3 to last-1 |
<subject> |
List of one or more subjects whose sphere files will be input. |
last |
<template_path> |
Full path to template file. If tempate already exists, it will be input, used to register subjects and new variables will be added to it. If it does not exist it will be created, and initial data created from the first subject. |
Required Flagged Arguments
None
Optional Flagged Arguments
Note: single-letter flags can be upper or lower case.
MMTable
Category |
Flag |
<Args> |
Description |
Input |
-sulc |
<othercurv> |
Sets curvature_names[1] (of 0..2) to othercurv. Default is 'sulc'. |
Input |
-infname |
<surffilename> |
Sets surface_names[0] = surffilename, and curvature_names[0] = surffilename'.H'. Default is 'inflated'. (Not sure what a '.H' file is or where it comes from. --GW). |
Input |
-O |
<surface_name> |
Sets a different surface_name for surface_names 1 and 2 (of 0,1,2), instead of default smoothwm. |
Input |
-overlay-dir |
<overlay_dir> |
Sets directory from which to read optional overlay file. Default 'label'. |
Input |
-sdir |
<subjects_dir> |
Set SUBJECTS_DIR to subjects_dir |
Template config |
-addframe |
<which_field where_in_atlas> |
Uses the two integer args to specify how to add a variable to the atlas (ie: template). |
Template config |
-nodefault |
|
Not sure the purpose of this option --GW |
Template config |
-overlay |
<overlay_file> |
Increases atlas_size by one (to makes space for additional template variable) and reads overlay file from {subject}/label/{overlay_file}. To change directory, use -overlay_dir option |
Template config |
-size |
<atlas_size> |
Sets the atlas (ie: template) to be able to contain data for atlas_size number of variables for each vertex. Default is atlas_size=3. |
Algorithm |
-A |
<navgs> |
Average curvature patterns navgs times |
Algorithm |
-annot |
<annot_name> |
Zero the median wall. Ie: Causes program to read annotation file from which to find vertices that belong to the medial wall so that these can be given a curvature of zero. Rationale? |
Algorithm |
-median |
|
Using median normalization (default is mean) |
Algorithm |
-nbrs |
<nbrs> |
Set neighborhood size to nbrs |
Algorithm |
-norot |
|
Help/usage info for this is wrong (--GW): |
Algorithm |
-rot |
|
-rot printout: 'rigidly aligning hemispheres before averaging.' |
Algorithm |
-S |
<scale> |
Scale 'parameterization' by scale (float). (If 'parameterization' refers to a complete surface worth of per-vertex values (ie: a template variable), is the idea here to scale all those variables by the same amount? --GW) |
Utility |
-?, -U |
|
print_usage() |
Utility |
-help, --help |
|
print_help() |
Utility |
-vector |
|
Prints some help for using Multiframe mode. Option presumably named 'vector' because multiframe mode means that the template has multiple values per vertex. |
Utility |
-version, --version |
|
print_version() |
Utility |
-W |
<optional int> |
Obsolete option. Ignored. |
Footer |
XXXXXXXXXXXXX |
|
Outputs
output |
?? |
Description
??
Examples
Example 1
??
description
Example 2
command foo -i f -o out -f fvalue
description
Bugs
None
See Also
mris_make_template, SurfaceRegAndTemplates
Links
Methods Description
??
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>