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
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