Index

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

othercommand1, othercommand2

Links

FreeSurfer, FsFast

Methods Description

??

References

References/Lastname###

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

BruceFischl