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 > <mailto: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 > <mailto: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 <mailto: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 > <mailto: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 > <mailto: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 <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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
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