Hi Bruce, I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files.
Thanks! On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Marja > > why are you converting at all? Why not just give one of the dicom files in > the correct series to recon-all directly? I don't think we've ever seen an > orientation problem if you process that way > > cheers > Bruce > > > On Tue, 14 Jun 2016, Marja Caverlé wrote: > > 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. 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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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