Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly.


On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser@zoho.com> wrote:

Hi,

I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.

Using:

mri_convert -it siemens -ot mgz 1.IMA test.mgz

I get the error message:

does not contain a Siemens ASCII header has this file been anonymised?

ERROR: cannot unpack mosiacs without ASCII header

The .IMA files have been taken straight from the scanner console.

If I try:

mri_convert -it dicom -ot mgz 1.IMA test.mgz

this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA.

 

Any suggestions on how to convert the Siemens .IMA files correctly?

 

Thanks,

Paul


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