Index

Name

mri_synthesize - Creates a synthetic FLASH image based on previously calculated T1 and proton density maps

Synopsis

mri_synthesize [options] <TR> <alpha (deg)> <TE> <T1 volume> <PD volume> <output volume>

Arguments

Positional Arguments

TR

Repetition time of synthetic image (ms)

alpha

Flip angle (degrees) of synthetic image

TE

Echo time (ms) of synthetic image

T1 volume

Path of previously calculated T1 volume (mgh or mgz formats)

PD volume

Path of previously calculated PD volume (mgh or mgz formats)

Output volume

Path for synthetic volume

Required Flagged Arguments

-flag1 arg1

brief description

detailed description (eg, help file information)

-flag2 arg2

brief description

detailed description (eg, help file information)

Optional Flagged Arguments

-w

Optimal gray/white matter contrast weighting

Outputs

Synthetic Volume

('mgh' format)

Description

This program will synthesize a flash acquisition based on previously computed T1/PD maps

Examples

Example 1

fdir = $subjects_dir/$subj/mri/flash

mri_synthesize -w 20 30 5 $fdir/T1.mg* $fdir/PD.mg* $fdir/../orig/orig.mgh

Description: This command takes the T1 and PD volumes (they can be either 'mgh' or 'mgz' (compressed) format), and creates an optimally weighted FLASH image with TR=20ms, flip_angle=30degrees, TE=5ms. The synthetic image is written in the $subjects_dir/$subj/mri/orig directory with 'mgh' format.

Bugs

None

See Also

mri_ms_fitparms (to compute T1/PD maps)

Links

FreeSurfer, FsFast

Methods Description

N/A

References

References/Lastname###

Reporting Bugs

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

Author/s

BruceFischl

mri_synthesize (last edited 2008-04-29 11:46:21 by localhost)