Greg,
mri_convert -help has a 'specifying the orientation' section which
describes the options for re-orienting. You could try adding this flag:
--out_orientation LAS
to output in radiological convention.
N.
On Tue, 2006-12-19 at 17:42 -0500, Kirk, Gregory wrote:
Hi All ,
I am using mri_convert to convert Siemens 30 direction diffusion data
into NIfTII for
proc. with fsl. mri_convert does it well except that it is a bit
problematic that it comes
out in neurological convention. Also the tools is fsl do not seem
capable to change the orientation to
radiological convention. I want to use a structural cooregistered to
the diffusion b0 to navigate for
placing seeds for stochastic tract processing. mri_convert takes my
Siemens structurals and puts them in NIfTI
files that are oriented completely wrong, upside down etcetera.
Obviously mri_convert knows how to read Siemens
structurals ... it's does it all the time for freefurfer processing.
So I take analyze 7.5 format structurals and it comes
out in radiological convention and fsl tools are incapable to change
these into neurological convention !
so a bit of a sticky wicket, of course it would be nice if fsl would
support it's own tools for data inport, but as far as I
know they do not. NIfTI code from COX et. al. is well.... as he puts
it himself Klingon software, Klingon's that fell on their head anyway.
it is not organized well enough to spend the time to see if anything
usable is there.
I guess the q-form or s-form are not set such that the fsl tools can
work with 7.5 or mri_convert produced files.
any way to get correctly oriented NIfTI structurals or to reorient the
diffusion data to radiological.
cheerio
Greg.
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