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

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:

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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