Hi Bruce, When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best, Marja On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > What do you mean that FS did not accept the dicom files? Can you provide a > command line and terminal output? You can use dcmunpack -src /path/to/dicom > to get a list of the series in a dicom folder > > > On 6/13/16 9:57 PM, Marja Caverlé wrote: > > 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>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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