mri_convert options - Freesurfer

31 Oct 2006


      Hi,
Currently we've been converting from .img to .mgz format using the
following syntax:
mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz
s1501p.img mri/orig/001.mgz
It came to my attention today that the values we used for TI, TE, and TR
are all actually in ms, and correspond to the Siemen's Vision use of the
terms TI and TR for the MRPAGE sequence.  This is quite different from how
TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and
Trio Siemens platform.  Furthermore, we have actually been applying these
values to Vision FLASH data as well, for which TI is irrelevant, and the
TR and flip were different.  Basically, we have just been confused in our
use of mri_convert.
So, this raises a couple questions:
1) Are the TI, TE, TR and flip parameters important to mri_convert?  How
are they used?  Are they used in any manner in the subsequent Freesurfer
processing stream?  We wonder if they are not important, since the current
documention lists TR as an option, but doesn't mention TI, TE, or flip as
options.
2) If these parameters are important in some manner how would the use of
such grossly incorrect values affect the results?
So basically, we are wondering what parameters, if any, are truly
necessary as part of mri_convert?  And do we (gasp) need to consider
rerunning the stream from stage 1...
Thanks!
Derin