> We are using Freesurfer5.3 on os x 10.8. >
> On 6 Dec 2013, at 2:19 pm, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > 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> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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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