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| * $Date: 2007/02/13 12:20:16 $ * $Revision: 1.23 $ |
* $Date: 2006/12/29 02:09:07 $ * $Revision: 1.25 $ |
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| = Purpose = Xxx |
= Overview = Reads data from two or more subjects and creates a template file for volumes. (as opposed to [[mris_make_template]] which makes a template for registering surfaces.) |
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| mri_make_template subject1 [subject2 ...] output | mri_make_template [Flagged args] subject1 [subject2...] ouput_template_path |
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| || subject1 || description || || subject2 || description || || output|| description || |
||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''|| ||<^>1 to last-1||<^> <subject> ||<^>List of one or more subjects to input|| ||<^>last||<^> <Out_fname> ||<^>Full path to output template file.|| |
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| ||<^>Input||<^> -sulc||<^> <othercurv> ||<^>Sets curvature_names[1] (of 0..2) to othercurv. Default is 'sulc'.|| ||<^>Input||<^>-infname||<^> <surffilename> ||<^#FFFF80>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|| ||<^>Atlas config||<^>-addframe||<^> <which_field where_in_atlas> ||<^>Uses the two integer args to specify how to add a variable to the atlas.[[BR]] [[BR]]which_field specifies the variable to add, with the meaning of the number determined by the list you can get from the vector option.[[BR]][[BR]]where_in_atlas tells what order to place the new field/ Locations 0..2 are already occupied by the default variables.|| ||<^>Atlas config||<^>-nodefault||<^> ||<^>Not sure the purpose of this option --GW[[BR]][[BR]]base_default=0;[[BR]][[BR]]atlas_size = 0;[[BR]][[BR]]parms->nfields=0;[[BR]][[BR]]for (n=0;n<3;n++)[[BR]][[BR]]InitFieldLabel(&parms->fields[n]);|| ||<^>Atlas config||<^>-overlay||<^> <overlay_file> ||<^>Increases atlas_size by one (to makes space for additional atlas variable) and reads overlay file from {subject}/label/{overlay_file}. To change directory, use -overlay_dir option|| ||<^>Atlas config||<^>-size||<^> <atlas_size> ||<^>Sets the atlas 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||<^> ||<^#FFFF80>Help/usage info for this is wrong (--GW):[[BR]][[BR]]Usage: -norot : 'align before averaging'[[BR]][[BR]]-norot printout: 'not aligning hemispheres before averaging'[[BR]][[BR]]What source code appears to do:[[BR]][[BR]]If -norot is selected, program appears to skip performing rigid alignment of subject's surface to template before averaging.[[BR]][[BR]]This appears to be the default, which is surprising because in addition to the Usage info describing this option wrongly, Usage does not mention the '-rot' option.|| ||<^>Algorithm||<^>-rot||<^> ||<^>-rot printout: 'rigidly aligning hemispheres before averaging.' [[BR]]ie: DO perform rigid alignment of subject's surface to template before averaging.[[BR]][[BR]]What source code appears to do:[[BR]][[BR]]For multiframes situation: always perform rigid alignment.[[BR]][[BR]]For NOT multiframe situation: perform rigid alignment for all subjects except for the first. (Presumably the first subject is used to create the initial template data?)|| ||<^>Algorithm||<^>-S||<^> <scale> ||<^>Scale 'parameterization' by scale (float). (If 'parameterization' refers to a complete surface worth of per-vertex values (ie: an atlas 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.|| |
||<^>Input||<^>-open||<^> <open> ||<^>Open input volume {open} times|| ||<^>Input||<^>-sdir||<^> <subjects_dir> ||<^>Sets SUBJECTS_DIR instead of default|| ||<^>Input||<^>-T1||<^> <T1_name> ||<^>Reads T1 volume from directory T1_name. (Or file, presumably?)|| ||<^>Output||<^>-B||<^> <binary_name> ||<^>Generates binary template from {binary_name} volume|| ||<^>Output||<^>-novar||<^> ||<^>Disables writing of variance estimates|| ||<^>Output||<^>-S,-V||<^> <var_fname> ||<^>Writes variances|| ||<^>Output||<^>-statsonly||<^> ||<^>|| ||<^>Output||<^>-X||<^> <xform_mean_fname, xform_covariance_fname> ||<^>Writes means and covariances of xforms|| ||<^>Algorithm||<^>-binarize||<^> <binarize (int)> ||<^>Binarizes input volume with thresh= binarize|| ||<^>Algorithm||<^>-erode||<^> <erode> ||<^>Erodes input volume {erode} times|| ||<^>Algorithm||<^>-N||<^> ||<^>Don't use transform on first volume|| ||<^>Algorithm||<^>-smooth||<^> <smooth (float)> ||<^>Smooths output with Gaussian sigma= smooth|| ||<^>Algorithm||<^>-T||<^> <transform_fname> ||<^>Applies transformation {transform_fname} to each volume|| ||<^>Utility||<^>-?,-U||<^> ||<^>Print usage|| |
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| ?? | Not sure what kind of template this produces, nor what registration is expected upstream from the is program. --GW |
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| ["mris_make_template"] | [[mris_make_template]] |
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| ["References/Lastname###"] | [[References/Lastname###]] |
Index
Contents
Software version described:
- $Date: 2006/12/29 02:09:07 $
- $Revision: 1.25 $
- Use usage or version option to see version you are using
Name
mri_make_template
Overview
Reads data from two or more subjects and creates a template file for volumes. (as opposed to mris_make_template which makes a template for registering surfaces.)
Synopsis
mri_make_template [Flagged args] subject1 [subject2...] ouput_template_path
Arguments
Positional Arguments
Posn |
<Argname> |
Description |
1 to last-1 |
<subject> |
List of one or more subjects to input |
last |
<Out_fname> |
Full path to output template file. |
Required Flagged Arguments
None
Optional Flagged Arguments
Category |
Flag |
<Args> |
Description |
Input |
-open |
<open> |
Open input volume {open} times |
Input |
-sdir |
<subjects_dir> |
Sets SUBJECTS_DIR instead of default |
Input |
-T1 |
<T1_name> |
Reads T1 volume from directory T1_name. (Or file, presumably?) |
Output |
-B |
<binary_name> |
Generates binary template from {binary_name} volume |
Output |
-novar |
|
Disables writing of variance estimates |
Output |
-S,-V |
<var_fname> |
Writes variances |
Output |
-statsonly |
|
|
Output |
-X |
<xform_mean_fname, xform_covariance_fname> |
Writes means and covariances of xforms |
Algorithm |
-binarize |
<binarize (int)> |
Binarizes input volume with thresh= binarize |
Algorithm |
-erode |
<erode> |
Erodes input volume {erode} times |
Algorithm |
-N |
|
Don't use transform on first volume |
Algorithm |
-smooth |
<smooth (float)> |
Smooths output with Gaussian sigma= smooth |
Algorithm |
-T |
<transform_fname> |
Applies transformation {transform_fname} to each volume |
Utility |
-?,-U |
|
Print usage |
Footer |
XXXXXXXXXXXXX |
|
Outputs
output |
?? |
Description
Not sure what kind of template this produces, nor what registration is expected upstream from the is program. --GW
Examples
Example 1
??
description
Example 2
command foo -i f -o out -f fvalue
description
Bugs
None
See Also
Links
Methods Description
??
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>