| Deletions are marked like this. | Additions are marked like this. |
| Line 22: | Line 22: |
| || invol || input volume || | || invol || input volume || |
| Line 24: | Line 24: |
| || outvol || output volume || | || outvol || output volume || |
| Line 32: | Line 32: |
|
|| -mask brainmask || || || -invert-and-save gcamfile || || || -dist distance || || || -regularize regularize || || || -regularize-mean regularizemean || || || -scale_smoothness smoothness || || || -nobright || || || -renormalize || || || -read_lta || || || -smoothness smoothness || || || -samples samples || || || -nsmall nsmall || || || -fixed || || || -optimal || || || -noneg noneg || || || -wm || || || -min_avgs <n> || || || -tl || || || -relabel relable || || || -relabel_avgs relable_avgs || || || -reset_avgs reset_avgs || || || -vf vf_fname || || || -diag diagfname || || || -tr tr || || || -te te || || || -example T1 seg || || || -<no>bigventricles || || |
|| -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 || |
| Line 60: | Line 60: |
| || -secondpassrenorm || || | || -secondpassrenorm || perform 2nd-pass renormalization || |
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>