Hi Jon, I am also confused about this whole discussion. It seems from what you said earlier that at some point you have been able to run freesurfer on your images. You did not use the -i flag back then, but somehow managed to get from the original dicom (via nifti, via some mri_convert command) to some image that free surfer was able to use.
Just do the same thing here and then once that is done, run the base and long stream on top of it. Best, Martin On Jul 8, 2013, at 2:45 PM, Jonathan Holt <whats...@umich.edu> wrote: > I potentially have access to dicoms. My PI was confused as we're using GE 2D > dcm images with 126 images per timepoint, he wasn't sure how to have them > organized for a test run. > > > On Jul 8, 2013, at 2:20 PM, Allison Stevens Player wrote: > >> I see now. If the orientation information is incorrect, this will continue >> to be a problem. It sounds like you have access to the dicoms? If so, it's >> better to wait and use those. >> Allison >> >> On Mon, 8 Jul 2013, Jonathan Holt wrote: >> >>> Allison I'm running the following >>> >>> recon-all -all -s <subjID> -i path/to/nifti >>> >>> attatched is the error recon log >>> >>> I've already gone over this with bruce, martin. It seems as if the 001.mgz, >>> orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming >>> straight out of the nifti files I've passed and these mgz's are generated >>> before the recon-all process exits with errors. >>> >>> >>> >>> >>> On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote: >>> >>>> In short, the answer is yes. The 2nd and 3rd steps will take the subject >>>> ID and find the relevant files. But I would expect the first step to take >>>> nifti just fine. Can you send the command you are running? >>>> >>>> On Mon, 8 Jul 2013, Jonathan Holt wrote: >>>> >>>>> As I'm having trouble importing nifti files into the first step of the >>>>> longitudinal work flow, I'm wondering if I can use volumes generated from >>>>> recon-all -s <subjID> for the second and third steps of the workflow. >>>>> >>>>> jon >>>>> _______________________________________________ >>>>> 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 >> >> >> 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 > > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
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