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> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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