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| <<Navigation(children)>> '''Index''' <<TableOfContents>> |
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| mri_register - ? | mri_register - high-dimensional alignment with canonical atlas |
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| mri_register [in brain] [ref brain] [output file name] | mri_register [options] invol refvol outvol |
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| = Positional Arguments = || [in brain] || ? || || [ref brain] || ? || || [output file name] || ? || |
= Arguments = == Positional Arguments == || invol || input volume || || refvol || reference volume || || outvol || output volume || |
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| = Required Flagged Arguments = none |
== Required Flagged Arguments == None |
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| = Optional Flagged Arguments = none |
== Optional Flagged Arguments == || -align || || || -T lta || || || -mask <brainmask> || use MR volume brainmask to mask input volume || || -invert-and-save <gcamfile> || load, invert and save gcamfile, then exit|| || -dist distance || l_dist = distance || || -regularize <reg> || regularize variance to be sigma +reg (noise) || || -regularize-mean <regmean> || regularize means to be regmean u(global) + (1-regmean) u(r)|| || -scale_smoothness <bool> || scale (or not scale) smooothness coefficient (default=1) setting npasses=2 || || -nobright || remove bright non-brain structures || || -renormalize || renormalize GCA to MAP estimate of means|| || -read_lta || read LTA from <base-name>.lta || || -smoothness <real> || l_smoothness = real || || -samples <cpfile> || write control points to <cpfile> || || -nsmall <int> || allow int small steps before terminating integration|| || -fixed || use fixed time-step integration || || -optimal || use optimal time-step integration || || -noneg bool || allow or not allow temporary folds during numerical minimization || || -wm || register white matter in initial pass || || -min_avgs <n> || setting min # of averages to n (default 0) || || -tl <file> ||read temporal lobe atlas from <file> || || -relabel bool ||relabel or not relabel nodes with MAP estimates || || -relabel_avgs real || relabel nodes with MAP estimates at avgs=real || || -reset_avgs real || reset metric properties at avgs=real || || -vf <vf_fname> || write vector field to <vf_fname> || || -diag <diagfname> || open diagfname for writing || || -tr real || use TR=real msec || || -te real || use TE=real msec || || -example <T1> <seg> || use T1 and seg as example T1 and segmentations respectively || || -<no>bigventricles || handle expanded ventricles || || -uncompress || || || -secondpassrenorm || perform 2nd-pass renormalization || |
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| || output file name || ? || | || outvol || output volume|| |
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| description | ?? |
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| command foo -i f -o out description |
{{{ mri_ca_register -align -mask brainmask.mgz \ -T transforms/talairach.lta norm.mgz \ $FREESURFER_HOME/average/RB_all_2006-02-15.gca \ transforms/talairach.m3z }}} |
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| command foo -i f -o out -f fvalue description |
?? |
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| ["othercommand1"], ["othercommand2"] | [[othercommand1]], [[othercommand2]] |
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| description description |
?? |
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| ["References/Lastname###"] | [[References/Lastname###]] |
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| JaneSmith | BruceFischl |
Index
Contents
Name
mri_register - high-dimensional alignment with canonical atlas
Synopsis
mri_register [options] invol refvol outvol
Arguments
Positional Arguments
invol |
input volume |
refvol |
reference volume |
outvol |
output volume |
Required Flagged Arguments
None
Optional Flagged Arguments
-align |
|
-T lta |
|
-mask <brainmask> |
use MR volume brainmask to mask input volume |
-invert-and-save <gcamfile> |
load, invert and save gcamfile, then exit |
-dist distance |
l_dist = distance |
-regularize <reg> |
regularize variance to be sigma +reg (noise) |
-regularize-mean <regmean> |
regularize means to be regmean u(global) + (1-regmean) u(r) |
-scale_smoothness <bool> |
scale (or not scale) smooothness coefficient (default=1) setting npasses=2 |
-nobright |
remove bright non-brain structures |
-renormalize |
renormalize GCA to MAP estimate of means |
-read_lta |
read LTA from <base-name>.lta |
-smoothness <real> |
l_smoothness = real |
-samples <cpfile> |
write control points to <cpfile> |
-nsmall <int> |
allow int small steps before terminating integration |
-fixed |
use fixed time-step integration |
-optimal |
use optimal time-step integration |
-noneg bool |
allow or not allow temporary folds during numerical minimization |
-wm |
register white matter in initial pass |
-min_avgs <n> |
setting min # of averages to n (default 0) |
-tl <file> |
read temporal lobe atlas from <file> |
-relabel bool |
relabel or not relabel nodes with MAP estimates |
-relabel_avgs real |
relabel nodes with MAP estimates at avgs=real |
-reset_avgs real |
reset metric properties at avgs=real |
-vf <vf_fname> |
write vector field to <vf_fname> |
-diag <diagfname> |
open diagfname for writing |
-tr real |
use TR=real msec |
-te real |
use TE=real msec |
-example <T1> <seg> |
use T1 and seg as example T1 and segmentations respectively |
-<no>bigventricles |
handle expanded ventricles |
-uncompress |
|
-secondpassrenorm |
perform 2nd-pass renormalization |
Outputs
outvol |
output volume |
Description
??
Examples
Example 1
mri_ca_register -align -mask brainmask.mgz \
-T transforms/talairach.lta norm.mgz \
$FREESURFER_HOME/average/RB_all_2006-02-15.gca \
transforms/talairach.m3z
Example 2
??
Bugs
None
See Also
Links
Methods Description
??
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>