Hi Ruopeng, I am very sorry since I think you would like to figure out why freeview did not take my DICOM's, but due to privacy issues I have deleted the DICOM's after the recon -all (on the niftis) was completed without any errors. Basically when I selected the files, nothing happened, while when I selected the nifti it loaded the scan. No error or anything like that.
Best, Marja On Tue, Jun 14, 2016 at 11:51 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > Would it be possible to send us a file? > > Best, > Ruopeng > > On Jun 14, 2016, at 8:52 AM, Marja Caverlé <marja.cave...@gmail.com> > wrote: > > Hi Bruce, > > I did not get any error message, the page just remained empty after > selecting the files. Maybe my files were the reason why it didn't work. > > Best, > > Marja > > On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu > > wrote: > >> freeview works fine with most dicoms. Do you get an error message? >> >> On Tue, 14 Jun 2016, Marja Caverlé wrote: >> >> 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> >>> 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. >> >> > _______________________________________________ > 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 > 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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