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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:

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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.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

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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:

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Is 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

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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:

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Which 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

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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.

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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
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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