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.