|
Size: 6599
Comment:
|
← Revision 19 as of 2008-04-29 11:45:52 ⇥
Size: 3039
Comment: converted to 1.6 markup
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 9: | Line 9: |
| [[Navigation(children)]] | <<Navigation(children)>> |
| Line 11: | Line 11: |
| [[TableOfContents]] | <<TableOfContents>> |
| Line 14: | Line 14: |
| * $Date: 2007/02/13 12:20:16 $ * $Revision: 1.23 $ |
* $Date: 2006/12/29 02:09:07 $ * $Revision: 1.25 $ |
| Line 21: | Line 21: |
| = Purpose = 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. Note: Descriptions below 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 parcellations. (See ["mris_ca_train"].) |
= 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.) |
| Line 27: | Line 25: |
| mri_make_template subject1 [subject2 ...] output | mri_make_template [Flagged args] subject1 [subject2...] ouput_template_path |
| Line 31: | Line 29: |
| Line 33: | Line 30: |
| ||<^>1||<^> <hemi> ||<^>lh or rh|| ||<^>2||<^> <sphere_name> ||<^>Name of sphere surface to read from each subject. Actual filepath will be:[[BR]][[BR]]{subject}/surf/{sphere_name}.{hemi}|| ||<^>3 to last-1||<^> <subject> ||<^>List of one or more subjects whose sphere files will be input.|| ||<^>last||<^> <template_name> ||<^>Name of template. 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.|| |
||<^>1 to last-1||<^> <subject> ||<^>List of one or more subjects to input|| ||<^>last||<^> <Out_fname> ||<^>Full path to output template file.|| |
| Line 42: | Line 37: |
| Note: single-letter flags can be upper or lower case.[[BR]] |
|
| Line 45: | Line 38: |
| ||<^>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|| |
| Line 72: | Line 58: |
| ?? | Not sure what kind of template this produces, nor what registration is expected upstream from the is program. --GW |
| Line 89: | Line 75: |
| ["mris_make_template"] | [[mris_make_template]] |
| Line 100: | Line 86: |
| ["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>