No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct.
Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > so you convert from dicom to nifti, then view in freeview and you think > that the anatomical orientations are incorrect? That should definitely not > be the case > > > On Tue, 14 Jun 2016, Marja Caverlé wrote: > > Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer >> and fsl. And there they seemed to match. >> So my question is; is there a possibility that dimensions are swapped >> during >> the recon -all? If not, then I am sure R=R and L=L. >> >> Thanks! >> >> On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Marja >> >> what did you visualize it in? I would suggest freeview >> >> cheers >> Bruce >> On Tue, 14 Jun 2016, Marja Caverlé wrote: >> >> Hi Bruce, >> >> I converted the images with MRIconvert, then I >> swapped them in FSL with >> swapdim. >> I checked the images by opening the original dicoms >> and the converted >> niftis, and then visually compared them (since the >> heads are not very >> symmetrical that was not too hard). >> >> Best, >> >> Marja >> >> >> On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Marja >> >> how did you swap them? And more importantly, >> how did you check >> that the orientations were correct after >> conversion? >> >> cheers >> Bruce >> >> >> On Mon, 13 Jun 2016, Marja Caverlé wrote: >> >> Hi guys, >> >> Just a quick question; I have converted >> my original >> DICOMs into niftis. >> After the conversion I manually checked >> whether the >> orientations were still >> the same, and they were not, so I >> swapped them. >> After this I did a recon >> -all. >> A lot of my results are at one side >> while I expected >> them in the other >> hemisphere. Is there any chance that the >> recon -all >> swapped left and right? >> How to check for this? I just want to be >> sure that I >> am really talking about >> the right hemisphere. >> >> Thanks! >> >> Best, >> >> Marja >> >> >> _______________________________________________ >> 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 > > > 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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