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.

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)

Links

FreeSurfer, FsFast

Methods Description

description
description

References

Reporting Bugs

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

Author/s

MartinReuter

-Deletions are marked like this.
+Additions are marked like this.
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-|| argA || brief description || detailed description (eg, help file information)  ||

|| argB || brief description || detailed description (eg, help file information)  ||
+None
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-|| -flag1 arg1 || brief description || detailed description (eg, help file information) ||

|| -flag2 arg2 || brief description || detailed description (eg, help file information) ||
+|| - - 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 ||
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-|| -flag3 arg3 || brief description ||detailed description (eg, help file information) ||

|| -flag4 arg4 || brief description ||detailed description (eg, help file information) ||
+|| - - 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) ||
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-|| volume1 || description ||

|| volume2 || description ||
+See above
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-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.
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+Line 51:
-command foo -i f -o out
+{{{

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

}}}
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+Line 55:
-description
+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).
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-== Example 2 ==

command foo -i f -o out -f fvalue
+View results:

{{{

tkmedit -f mean.mgz -aux tp1tomean.mgz

}}}
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-description