But of course, Bruce says the .nii.gz format should have worked, so it does not need to be type mgz format. I would trust Bruce. Sorry for not cc'ing the mailing list earlier.
Thanks, John John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2 Begin forwarded message: > From: John Jan Drozd <john.dr...@gmail.com> > Date: 1 August, 2011 5:10:07 PM EDT > To: "Tax, C.M.W." <c.m.w....@student.tue.nl> > Subject: Re: [Freesurfer] Problem loading nii > > Hi, > > I believe the image must be type mgz format for Freesurfer. (For FSL it > needs to be type nii or nii.gz.) > > Try typing: > > gunzip t1.nii.gz > mri_convert t1.nii t1.mgz > tkmedit -f t1.mgz > > John > > John Drozd > Post-Doctoral Fellow > Robarts Research Institute > University of Western Ontario > London, Ontario, Canada > http://publish.uwo.ca/~jdrozd2 > > > On 2011-08-01, at 4:55 PM, "Tax, C.M.W." <c.m.w....@student.tue.nl> wrote: > >> Dear Sir/Madam, >> >> I would like to use freesurfer for cortical flattening, working with the nii >> format. When I try to load the nii.gz file as described on >> http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html, I get the following >> error: >> >> student@BMT-PC125:~$ tkmedit -f t1.nii.gz >> niiRead(): error opening file ./t1.nii.gz >> >> >> Error: Loading volume t1.nii.gz >> >> Couldn't read the anatomical volume. >> >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> >> >> This image t1.nii.gz was obtained by converting DICOM images with dcm2nii. I >> also tried to load a example dataset downloaded from >> http://nifti.nimh.nih.gov/nifti-1/data, but still I get the same error. FSL >> was able to load both datasets without problems. >> >> Please could you help me with this problem? >> >> Thank you in advance, >> >> Kindest Regards >> >> _______________________________________________ >> 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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