does it load ok in freesurfer (in tksurfer)? What error do you get in AFNI/FSL? If it
On Mon, 6 Feb 2012, Omer Tal wrote: > Hey Doug, > > Here is what I type it the terminal and what pops back at me. The error > shows up later when trying to load (either though AFNI or FSL). > > mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 241 --s > 111123 --hemi lh > > srcsubject = 111123 > srcval = test.mgh > srctype = > trgsubject = 111123 > trgval = test.nii > trgtype = > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > OKToRevFaceOrder = 1 > Reading source surface reg > /home/otal/raweegmeg/structuralDB//111123/surf/lh.sphere.reg > Loading source data > INFO: trgsubject = srcsubject > Saving target data > Reshaping 241 (nvertices = 157373) > Saving to test.nii > > Thank you, > Omer Tal > > > >> what's your command line and terminal output? >> >> Omer Tal wrote: >>> 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 >>>> >>>> >>>> >>> >>> >>> >> >> -- >> 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 >> > > _______________________________________________ > 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
