Tried both, but neither gave a proper nii image. Any other ideas?
Omer Tal > That particular number factors to 241 and 653, so use one of those as > the reshape factor to surf2surf. > doug > > Omer Tal wrote: >> Hey Doug, >> >> I believe for this patient/hemisphere the number of vertices is 157373. >> >> What is the workaround in the case my number of vertices is unluckily a >> prime? >> >> Thank you, >> Omer Tal >> >> >> >>> Hi Omar, how many vertices? The reshape only works if the number is not >>> prime (actually the largest prime factor has to be less than 2^15. >>> doug >>> >>> Omer Tal wrote: >>> >>>> 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 >>>> >>>> >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
