External Email - Use Caution good to hear. looking forward to it. any estimation as to when it will be ready?
Shachar On Mon, 24 Dec 2018 at 14:25, Glasser, Matthew <glass...@wustl.edu> wrote: > External Email - Use Caution > > We’re working on a FS 6.0+ compatible version of the HCP pipelines and > FreeSurfer that is almost ready. > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shachar Gal < > gal.shac...@gmail.com> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, December 24, 2018 at 3:12 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Ido Tavor <idota...@gmail.com>, Niv Tik <niv...@gmail.com> > Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all > > External Email - Use Caution > > yes, it is version 5.3.0-HCP > fsbuilds answered that I should upgrade to version 6, but im afraid that > it lacks the changes you made so the version will suit the HCP Pipelines... > > what do you suggest? > > thanks, > Shachar > > On Sun, 23 Dec 2018 at 17:00, Shachar Gal <gal.shac...@gmail.com> wrote: > >> Sorry, out of the office for the day. I'll get back to you about it >> tomorrow >> >> Shachar >> >> On Sun, Dec 23, 2018, 16:56 Glasser, Matthew <glass...@wustl.edu> wrote: >> >>> External Email - Use Caution >>> >>> Is that FreeSurfer 5.3? >>> >>> Matt. >>> >>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shachar Gal >>> <gal.shac...@gmail.com> >>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Date: Sunday, December 23, 2018 at 8:35 AM >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all >>> >>> External Email - Use Caution >>> >>> this is my Freesurfer version - >>> freesurfer-i386-apple-darwin10.8.0-stable5-20130513 >>> >>> and I think the update to macOS Mojave was after successfully running >>> the pipeline. >>> you think this could be the issue? should I just upgrade my freesurfer? >>> >>> thanks >>> >>> On Sun, 23 Dec 2018 at 16:28, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Which version of FreeSurfer is this and did you do some OS upgrade in >>>> between? >>>> >>>> Matt. >>>> >>>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shachar >>>> Gal <gal.shac...@gmail.com> >>>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>>> Date: Sunday, December 23, 2018 at 8:24 AM >>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>>> Subject: [Freesurfer] mpr2mni305 failed, during recon-all >>>> >>>> External Email - Use Caution >>>> >>>> hello, >>>> I'm running the hcp's FreeSurfer pipeline, and for some reason, after >>>> working successfully several times, on different subjects, im getting this >>>> error: >>>> *** >>>> /Users/georgieboy/Research/Piano/test/222/222/mri >>>> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 >>>> --no-rescale --i orig.mgz --o orig_nu.mgz \n >>>> \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n >>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log >>>> Darwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri >>>> Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 >>>> >>>> recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018 >>>> *** >>>> >>>> the information in the talairach_avi.log is as follows: >>>> >>>> *** >>>> dyld: Symbol not found: ___keymgr_global >>>> Referenced from: /Applications/freesurfer/bin/gauss_4dfp >>>> Expected in: /usr/lib/libSystem.B.dylib >>>> in /Applications/freesurfer/bin/gauss_4dfp >>>> Abort >>>> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 >>>> ERROR: mpr2mni305 execution aborted >>>> *** >>>> >>>> to be clear, this - /usr/lib/libSystem.B.dylib exists exactly where is >>>> was expected... >>>> >>>> the input image, orig.mgz, looks fine and is in 1 mm res... >>>> so im having trouble getting to the bottom of the error. >>>> >>>> thanks in advance, >>>> Shachar >>>> >>>> >>>> ------------------------------ >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. If you >>>> are not the intended recipient, be advised that any unauthorized use, >>>> disclosure, copying or the taking of any action in reliance on the contents >>>> of this information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ------------------------------ >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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