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
External Email - Use Caution
Which version of FreeSurfer is this and did you do some OS upgrade in between?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:24 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.ilhttp://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.
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 glasserm@wustl.edu wrote:
External Email - Use CautionWhich version of FreeSurfer is this and did you do some OS upgrade in between?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal < gal.shachar@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 Cautionhello, 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
External Email - Use Caution
Is that FreeSurfer 5.3?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:35 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 <glasserm@wustl.edumailto:glasserm@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:24 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.ilhttp://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.edumailto: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.
External Email - Use Caution
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 glasserm@wustl.edu wrote:
External Email - Use CautionIs that FreeSurfer 5.3?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal < gal.shachar@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 Cautionthis 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 glasserm@wustl.edu wrote:
External Email - Use CautionWhich version of FreeSurfer is this and did you do some OS upgrade in between?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal < gal.shachar@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 Cautionhello, 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
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.shachar@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 glasserm@wustl.edu wrote:
External Email - Use CautionIs that FreeSurfer 5.3?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal < gal.shachar@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 Cautionthis 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 glasserm@wustl.edu wrote:
External Email - Use CautionWhich version of FreeSurfer is this and did you do some OS upgrade in between?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal gal.shachar@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 Cautionhello, 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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 24, 2018 at 3:12 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ido Tavor <idotavor@gmail.commailto:idotavor@gmail.com>, Niv Tik <nivtik@gmail.commailto:nivtik@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.shachar@gmail.commailto:gal.shachar@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 <glasserm@wustl.edumailto:glasserm@wustl.edu> wrote:
External Email - Use Caution
Is that FreeSurfer 5.3?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:35 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 <glasserm@wustl.edumailto:glasserm@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:24 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.ilhttp://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.edumailto: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.edumailto: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.
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 glasserm@wustl.edu wrote:
External Email - Use CautionWe’re working on a FS 6.0+ compatible version of the HCP pipelines and FreeSurfer that is almost ready.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal < gal.shachar@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 idotavor@gmail.com, Niv Tik nivtik@gmail.com Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all
External Email - Use Cautionyes, 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.shachar@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 glasserm@wustl.edu wrote:
External Email - Use CautionIs that FreeSurfer 5.3?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal gal.shachar@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 Cautionthis 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 glasserm@wustl.edu wrote:
External Email - Use CautionWhich version of FreeSurfer is this and did you do some OS upgrade in between?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal gal.shachar@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 Cautionhello, 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
External Email - Use Caution
After the holidays.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 24, 2018 at 8:14 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all
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 <glasserm@wustl.edumailto:glasserm@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 24, 2018 at 3:12 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ido Tavor <idotavor@gmail.commailto:idotavor@gmail.com>, Niv Tik <nivtik@gmail.commailto:nivtik@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.shachar@gmail.commailto:gal.shachar@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 <glasserm@wustl.edumailto:glasserm@wustl.edu> wrote:
External Email - Use Caution
Is that FreeSurfer 5.3?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:35 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 <glasserm@wustl.edumailto:glasserm@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.commailto:gal.shachar@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, December 23, 2018 at 8:24 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.ilhttp://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.edumailto: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.edumailto: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.edumailto: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@nmr.mgh.harvard.edu
-
Glasser, Matthew -
Shachar Gal