Hey Bruce, Thank you for the prompt response.
The line is as follows: mri_convert -it mgh -ot nii test.mgh test.nii. Since I do agree that the issue is arising from the NIFTI bit limit, i tried doug's suggestion of mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 6 --s subject_name --hemi lh But it doesn't seem to solve the problem. even though now i can load it through FSL without it failing and quitting, the image is faulty w/ over 78,000 data points in the X direction, none in Y, and 240 in Z. At this point, Doug told him to send the file in and no more follow-up is shown... Please advise. Thank you very much, Omer Tal UCSD Keck Center for Functional MRI > Hi Omer > > what file are you trying to convert? What is your entire command line > with output and what problems do you have? Nifti unfortunately only allows > 16 bits for the width/height/depth/nframes, so surface overlays can't > usually fit as nvertices x 1 x 1 x nframes since nvertices > 2^16 (or 2^15 > signed). > > cheers > Bruce > > > On Mon, 6 Feb 2012, Omer > Tal wrote: > >> Hey there, >> >> I am trying to convert an mgh file I created into an nii volume so I can >> load it in AFNI. I was trying to use mri_convert, which I have used >> previously to make nii volumes from my aparc+aseg and it worked great, >> but >> this time the resulting file is faulty. >> >> I've noticed a previous thread where someone ran into a similar problem, >> and it had to do w/ too many vertices existing for NIFTI, and Doug >> suggested using mri_surf2surf, but it didn't work for that guy or me (at >> which point I think he was sending you files). >> >> Seems like it should be something common and trivial, but I can't get it >> too work, any suggestions? >> >> Thank you, >> Omer Tal >> UCSD Keck Center for Functional MRI >> _______________________________________________ >> 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. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
