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.
