Hey Doug,
I apologize, maybe I wasn't clear enough.
It DOESNT work in FSL. That would be enough for me if it did. It loads w/ out erroring out and quitting (as it did before the improper reshape), but it is obviously not a proper image anymore as it lost its three dimensions and nothing is displayed (see further explanation in previous e-mail to Bruce).
Would you like to review the file yourself? Maybe that could help clarify.
Thank you, Omer Tal
It appears to be working for both FS and FSL. If it is working in FS and FSL and not in AFNI, then there's not much we can do about it. The AFNI developers don't know about our tools, and we don't know about theirs. I suggest you send the file to the AFNI developers and ask why it does not load. doug
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 >>>>> greve@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 >>> greve@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 > greve@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 greve@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 greve@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