This may be a known problem. What version of FS are you using and what
is your platform?
doug
On 12/5/13 3:26 PM, prasser wrote:
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
<markplantz2...@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 <pras...@zoho.com
<mailto:pras...@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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