Can you upload a single dicom file to me? One should be enough On 12/06/2013 04:02 PM, Paul Rasser wrote: >> >> 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 > <mailto: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 >>> <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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto: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 >>> <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
