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[[Navigation(children)]] '''Index''' [[TableOfContents]] |
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| mri_ca_label [<options>] [input volume(s)] [xform] [gca file] [output volume] | mri_ca_label [<options>] invol1 [invol2 ...] xform gcafile outvol |
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= Positional Arguments = || [input volume(s)] || input volume(s) || || [xform] || ? || || [gca file] || ? || || [output volume] || output volume || |
= Arguments = == Positional Arguments == || invol1 [invol2 ...] || input volume(s) || || xform || transform file || || gcafile || ? || || outvol || output volume || |
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= Required Flagged Arguments = none |
== Required Flagged Arguments == None |
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| = Optional Flagged Arguments = | == Optional Flagged Arguments == |
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| || -wm [path] || use wm segmentation || | || -wm path || use wm segmentation || |
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|| -t1 [gca_t1] || use file to label thin temporal lobe || || -debug_voxel [x] [y] [z] || debug voxel || || -debug_node [x] [y] [z] || debug node || || -debug_label [int n] || debug label || || -tr [float n] || set TR in msec || || -te [float n] || set TE in msec || || -alpha [float n] || set alpha in radians || || -example [mri_vol] [segmentation] || use T1 (mri_vol) and segmentation as example || || -pthresh [float n] || use p threshold n for adaptive renormalization (default=.7) || || -niter [int n] || apply max likelihood for n iterations (default=2) || |
|| -t1 gca_t1 || use file to label thin temporal lobe || || -debug_voxel x y z || debug voxel || || -debug_node x y z || debug node || || -debug_label n || debug label || || -tr TR || set TR in msec || || -te TE || set TE in msec || || -alpha ALPHA || set alpha in radians || || -example mri_vol segmentation || use T1 (mri_vol) and segmentation as example || || -pthresh thresh || use p threshold n for adaptive renormalization (default=.7) || || -niter n || apply max likelihood for n iterations (default=2) || |
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| || -regularize [float n] || regularize variance to be sigma+nC(noise) || | || -regularize reg || regularize variance to be sigma+nC(noise) || |
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|| -fwm [mri_vol] || use fixed white matter segmentation from wm || || -mri [mri_vol] || write most likely MR volume to mri_vol || || -heq [mri_vol] || use histogram equalization from mri_vol || || -renorm [mri_vol] || renormalize using predicted intensity values in mri_vol || |
|| -fwm mri_vol || use fixed white matter segmentation from wm || || -mri mri_vol || write most likely MR volume to mri_vol || || -heq mri_vol || use histogram equalization from mri_vol || || -renorm mri_vol || renormalize using predicted intensity values in mri_vol || |
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|| -flash_params [filename] || use FLASH forward model and tissue params in filename to predict || || -renormalize [wsize] [iter] || reenorm class means [iter] times after initial label with window of [wsize] || || -r [mri_vol] || set input volume || |
|| -flash_params filename || use FLASH forward model and tissue params in filename to predict || || -renormalize wsize iter || reenorm class means [iter] times after initial label with window of [wsize] || || -r mri_vol || set input volume || |
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|| -a [int n] || mean filter n time to conditional densities || || -w [int n] [filename] || write snapshots of gibbs process every n times to filename || || -m [mri_vol] || use mri_vol to mask final labeling || || -e [int n] || expand || || -n [int n] || set max iterations to n (default=200) || || -f [int f] [float t] || filter labeled volume with threshold t (default=.5) mode filter f (default=0)times || |
|| -a n || mean filter n time to conditional densities || || -w n filename || write snapshots of gibbs process every n times to filename || || -m mri_vol || use mri_vol to mask final labeling || || -e n || expand || || -n n || set max iterations to n (default=200) || || -f f thresh || filter labeled volume with threshold thresh (default=.5) mode filter f (default=0)times || |
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| || output volume || ? || | || outvol || output volume || |
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| description | ?? |
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command foo -i f -o out description |
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command foo -i f -o out -f fvalue description |
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description description |
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| JaneSmith | BruceFischl |
Navigation(children) Index TableOfContents
Name
mri_ca_label - ?
Synopsis
mri_ca_label [<options>] invol1 [invol2 ...] xform gcafile outvol
Arguments
Positional Arguments
invol1 [invol2 ...] |
input volume(s) |
xform |
transform file |
gcafile |
? |
outvol |
output volume |
Required Flagged Arguments
None
Optional Flagged Arguments
-cross-sequence |
label a volume acquired with sequence different than atlas |
-nogibbs |
disable gibbs priors |
-wm path |
use wm segmentation |
-conform |
interpolate volume to be isotropic 1mm^3 |
-t1 gca_t1 |
use file to label thin temporal lobe |
-debug_voxel x y z |
debug voxel |
-debug_node x y z |
debug node |
-debug_label n |
debug label |
-tr TR |
set TR in msec |
-te TE |
set TE in msec |
-alpha ALPHA |
set alpha in radians |
-example mri_vol segmentation |
use T1 (mri_vol) and segmentation as example |
-pthresh thresh |
use p threshold n for adaptive renormalization (default=.7) |
-niter n |
apply max likelihood for n iterations (default=2) |
-novar |
do not use variance in classification |
-regularize reg |
regularize variance to be sigma+nC(noise) |
-nohippo |
do not auto-edit hippocampus |
-fwm mri_vol |
use fixed white matter segmentation from wm |
-mri mri_vol |
write most likely MR volume to mri_vol |
-heq mri_vol |
use histogram equalization from mri_vol |
-renorm mri_vol |
renormalize using predicted intensity values in mri_vol |
-flash |
use FLASH forward model to predict intensity values |
-flash_params filename |
use FLASH forward model and tissue params in filename to predict |
-renormalize wsize iter |
reenorm class means [iter] times after initial label with window of [wsize] |
-r mri_vol |
set input volume |
-h |
use GCA to histogram normalize input image |
-a n |
mean filter n time to conditional densities |
-w n filename |
write snapshots of gibbs process every n times to filename |
-m mri_vol |
use mri_vol to mask final labeling |
-e n |
expand |
-n n |
set max iterations to n (default=200) |
-f f thresh |
filter labeled volume with threshold thresh (default=.5) mode filter f (default=0)times |
Outputs
outvol |
output volume |
Description
??
Examples
Example 1
??
Example 2
??
Bugs
None
See Also
["othercommand1"], ["othercommand2"]
Links
Methods Description
??
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>