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> [options]

Arguments

Positional Arguments

None

Required Flagged Arguments

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

input volumes

movable volumes to be aligned to common mean/median template

- - template <template.mgz>

output template volume

mean/median image

Optional Flagged Arguments

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

output xforms to template (for each input)

- - warp <warp1.mgz> ...

map each input to template

- - weights <weights1.mgz> ...

output weights in target space

- - average #

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

- - iscale

allow also intensity scaling on high-res. (default no)

- - 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

- - sat <float>

set saturation for robust estimator (default 4.685)

- - uchar

set input type to UCHAR (with intensity scaling)

- - conform

conform volumes to 1mm vox (256^3)

- - debug

show debug output (default no debug output)

Outputs

See above

Description

Uses an iterative method to construct a mean/median volume and the robust rigid registration of all input images to the current mean/median.

Important Note: 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.

Examples

Example 1

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

Constructs a mean 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 (on highest resolution, once the images are well aligned).

View results:

tkmedit -f mean.mgz -aux tp1tomean.mgz

Bugs

None (of course)

See Also

mri_robust_register

Links

FreeSurfer, FsFast

Methods Description

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References

Reporting Bugs

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

Author/s

MartinReuter