Hi Greg,

first of all, you have to distinguish between the images being displayed upside down and them being misoriented. I assume that you are judging all of this with fslview, and I wish I had a dime for everytime someone came to me saying "mri_convert must be broken because my brains are upside down in fslview". fslview does not try to reorient the images and will happily show your brains upside down. To check whether the orientation is correct, look at the letters on the edges of the images. This indicate the direction that fslview believes the axes to be in. Or, even better, bring up the volume in tkmedit.

If you can show me that the oriention information (and so mri_convert) is wrong, I will surely fix it. If fslview is just showing them upside down, then this is not an mri_convert problem, and you should consult the FSL website for docs on how to shuffle the pixel data and headers around so that they display properly in fslview (look at avwswapdim and avwreorient).

doug




Kirk, Gregory wrote:
Message
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.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting