Ziad: any idea why Omer can open this file in tksurfer but not afni? Omer: I don't think you'll be able to load it in FSL since it's essentially a surface. Can you give us details about how you are trying to load it in AFNI? Are you using SUMA?
On Mon, 6 Feb 2012, Omer Tal wrote: > Sorry, that was the wrong error description (for the AFNI portion). > > It just says cannot open dataset test.nii > > Well, if it doesn't work on FSL or AFNI, I would guess it is the > conversion process from FreeSurfer. I don't think anyone on AFNI knows > mri_convert or mri_sruf2surf. > > Honestly just trying to get support for your product for a very simple > task, not sure where else I could find someone who would know how to use > FS outputs. > > Omer > > >> It sounds like it is doing the right thing. The geometry is going to be >> bogus because it is a surface. You should post to the AFNI list. >> doug >> >> Omer Tal wrote: >>> Hey Bruce, >>> >>> So the mgh file loads fine in tksurfer (shows proper map) for the given >>> subject, and so does its corresponding mgz (created from mri_convert). >>> >>> In FSL there is no physical error, but when loading in the nii file, the >>> X >>> location is in ~786XX instead of the typical -128 to 128 or something >>> close, Y has no slices to go through at all, and Z seems for the most >>> part >>> normal (240 slices centered at 0). >>> >>> When I was trying to load those in AFNI, it simply said "ncols 157373 in >>> volumes exceeds 32768" even though the reshape has been done. >>> >>> Thank you, >>> Omer Tal >>> >>> >>> >>>> 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 >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >> >> -- >> 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
