Re: [Freesurfer] bad file conversion
Hi Michael if it loaeds in freeview upside down then everything else will fail. What format did it start as? Best to use dicoms directly if you can, and avoid analyze. In any case, make sure that the directions are correct at the beginning (that is, for the file that you give to recon-all as the input). cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > > Hello, i was wondering if you could possibly help me with a subjects file > that has loaded badly. It not only loaded up-side down but looks as though > there are additional deficits that need correcting. Any tips or advice would > be greatly appreciated! > > > Kind regard, Michael > > > ___ 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.
Re: [Freesurfer] bad file conversion
Hi Bruce, i used a T1.nii file at the beginning and performed the standard recon-all to convert the file just like i did with the rest of them. I deleted the file and run it again but it still produced the same results using this method. Kind regards, Michael > On 3 Jul 2017, at 15:05, Bruce Fischl wrote: > > Hi Michael > > if it loaeds in freeview upside down then everything else will fail. What > format did it start as? Best to use dicoms directly if you can, and avoid > analyze. In any case, make sure that the directions are correct at the > beginning (that is, for the file that you give to recon-all as the input). > > cheers > Bruce > > > On Mon, 3 Jul 2017, Michael Davies wrote: > >> >> Hello, i was wondering if you could possibly help me with a subjects file >> that has loaded badly. It not only loaded up-side down but looks as though >> there are additional deficits that need correcting. Any tips or advice would >> be greatly appreciated! >> >> >> Kind regard, Michael >> >> >> > ___ > 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
Re: [Freesurfer] bad file conversion
Hi Michael where did you the T1.nii file come from? Do you have the dicoms that were used to create it? It will indeed continue to fail until you fix the file so that the anatomical directions are correct (which you can verify by viewing it in freeview) cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > Hi Bruce, i used a T1.nii file at the beginning and performed the standard > recon-all to convert the file just like i did with the rest of them. I > deleted the file and run it again but it still produced the same results > using this method. > > Kind regards, Michael > >> On 3 Jul 2017, at 15:05, Bruce Fischl wrote: >> >> Hi Michael >> >> if it loaeds in freeview upside down then everything else will fail. What >> format did it start as? Best to use dicoms directly if you can, and avoid >> analyze. In any case, make sure that the directions are correct at the >> beginning (that is, for the file that you give to recon-all as the input). >> >> cheers >> Bruce >> >> >> On Mon, 3 Jul 2017, Michael Davies wrote: >> >>> >>> Hello, i was wondering if you could possibly help me with a subjects file >>> that has loaded badly. It not only loaded up-side down but looks as though >>> there are additional deficits that need correcting. Any tips or advice would >>> be greatly appreciated! >>> >>> >>> Kind regard, Michael >>> >>> >>> >> ___ >> 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
