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'''Index'''
<<TableOfContents>>


= 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