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
