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  It is used for the MotionCorrection step in recon-all and for creating a within-subject template in the longitudinal stream (-base) in FreeSurfer.
It is used for the MotionCorrection step in recon-all and for creating a within-subject template in the longitudinal stream (-base) in FreeSurfer.

Index

Name

mri_robust_template - construct an unbiased robust template for longitudinal volumes

Synopsis

mri_robust_template --mov <tp1.mgz> <tp2.mgz> ... --template <template.mgz> --satit [options]

Description

This program constructs an unbiased robust template for longitudinal volumes (within modality, 6-7 DOF). It uses an iterative method to construct a mean/median volume and the robust rigid registration of all input images to the current mean/median.

It is used for the MotionCorrection step in recon-all and for creating a within-subject template in the longitudinal stream (-base) in FreeSurfer.

Important Note: For best performance the input images should all have the same intensity level! Good images are, for example, the T1.mgz and norm.mgz from the FreeSurfer stream.

Arguments

Positional Arguments

None

Required Flagged Arguments

- - mov <tp1.mgz> <tp2.mgz> ...

input movable volumes to be aligned to common mean/median template

- - template <template.mgz>

output template volume (final mean/median image)

  • One of the following is required for sensitivity:

- - sat <real>

set outlier sensitivity manually (e.g. '--sat 4.685' ). Higher values mean less sensitivity.

- - satit

auto-detect good sensitivity (recommended for head or full brain scans)

Optional Flagged Arguments

- - lta <tp1.lta> <tp2.lta> ...

output xforms to template (for each input)

- - mapmov <aligned1.mgz> ...

output images: map and resample each input to template

- - weights <weights1.mgz> ...

output weights (outliers) in target space

- - average <#>

construct template from: 0 Mean, 1 Median (default)

- - inittp <#>

use TP# for spacial init (default random), 0: no init

- - fixtp

map everthing to init TP# (init TP is not resampled)

- - iscale

allow also intensity scaling (default off)

- - iscalein <is1.txt> <is2.txt> ...

use initial intensity scales

- - iscaleout <is1.txt> <is2.txt> ...

output final intensity scales (will activate --iscale)

- - ixforms <t1.lta> <t2.lta> ...

use initial transforms (lta) on source ('id'=identity)

- - vox2vox

output VOX2VOX lta file (default is RAS2RAS)

- - leastsquares

use least squares instead of robust M-estimator (for testing only)

- - noit

do not iterate, just create first template

- - maxit <#>

iterate max # times (if #tp>2 default 6, else 5 for 2tp reg.)

- - highit <#>

iterate max # times on highest resolution (default 5)

- - epsit <real>

stop iterations when all tp transform updates fall below <real> (if #tp>2 default 0.03, else 0.01 for 2tp reg.)

- - subsample <#>

subsample if dim > # on all axes (default no subs.)

- - floattype

convert images to float internally (default: keep input type)

- - finalnearest

use nearest neighbor in final interpolation when creating average. This is useful, e.g., when -noit and --ixforms are specified and brainmasks are mapped.

- - doubleprec

double precision (instead of float) internally (large memory usage!!!)

- - debug

show debug output (default no debug output)

Outputs

See above

Examples

Example 1

mri_robust_template --mov tp1.mgz tp2.mgz tp3.mgz --template mean.mgz --lta tp1.lta tp2.lta tp3.lta --mapmov tp1tomean.mgz tp2tomean.mgz tp3tomean.mgz --average 0 --iscale --satit

Constructs a mean (--average 0) template from tp1,tp2 and tp3 and outputs the mean.mgz, the corresponding transforms (tp?.lta) and aligned images (tp?tomean.mgz). Intensity scaling is allowed, the saturation/sensitivity for outliers is automatically computed (only possible for full head or full brain images).

View results:

tkmedit -f mean.mgz -aux tp1tomean.mgz

Example 2

mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200

Is used in the recon-all stream for motion correction of several (here two: 001.mgz and 002.mgz) inputs. In this case all follow-ups are registered to the first input (as specified with --inittp 1 --fixtp --noit) and the rawavg.mgz is output as the median image (--average 1).

Bugs

None (of course)

See Also

mri_robust_register

Links

FreeSurfer, FsFast

References

Reporting Bugs

Report bugs to <freesurfer@nmr.mgh.harvard.edu>

Author/s

MartinReuter

mri_robust_template (last edited 2020-05-28 10:41:38 by DougGreve)