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 fischl@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 <fischl@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.
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