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| ARRRG -- just edited this page by mistake. In the process of restoring. Sorry! --GW 2008-01-21 |
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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 = | = Overview = |
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| mri_make_template subject1 [subject2 ...] output | mri_make_template Xxxx |
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| || subject1 || description || || subject2 || description || || output|| description || |
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| ||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''|| ||<^>Input||<^> -sulc||<^> <othercurv> ||<^>Sets curvature_names[1] = othercurv. Default is 'curv'.|| ||<^>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.|| ||<^>Footer||<^>XXXXXXXXXXXXX||<^> ||<^>|| |
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| BruceFischl, GrahamWideman | BruceFischl |
Navigation(children) Index TableOfContents
ARRRG -- just edited this page by mistake. In the process of restoring. Sorry! --GW 2008-01-21
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
Xxx
Synopsis
mri_make_template Xxxx
Arguments
Positional Arguments
Required Flagged Arguments
None
Optional Flagged Arguments
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"]
Links
Methods Description
??
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>