Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs.

Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way?

Thanks,
Paul

---- On Wed, 04 Dec 2013 22:11:27 -0800 Mark Plantz <markplantz2016@u.northwestern.edu> wrote ----

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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