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The patch (see text below) only directed me to replace a file in the freesurfer/gcc/lib directory, which I did. Do I also need to replace the make_average_subject and mri_aparc2aseg files in my freesurfer bin?

To patch the existing 6.0.0 release you may need administrator privileges to do the following:

1) Remove your existing Freeview.app application bundle by sending it to the trash (and then emtying the trash).
   You can also do this from the terminal by cd'ing to the top level ./freesurfer subdirectory and then doing,
   "rm -rf Freeview.app". 

2) Copy the new Freeview.app.zip to where your old Freeview.app was located aund uncompress it (so it becomes
   the replacement Freeview.app in your current freesrufer installation).

3) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing freesurfer installation.

4) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch archive to /freesurfer/lib/gcc/lib in your current
   freesurfer installtion.

5) Try running the Freeview.app and loading a volume with it.

On Mon, Apr 5, 2021 at 6:43 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
It looks like you are still using the old make_average_subject as the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that those are really the patches?

On 3/29/2021 12:52 PM, Jordan Mullins wrote:

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Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins <jordan.mullins@email.ucr.edu> wrote:
Yes! Results attached.

On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you run
ls -l $FREESURFER_HOME/bin/mri_aparc2aseg $FREESURFER_HOME/bin/make_average_subject
and send the result?

Also, the result of
which mri_aparc2aseg
which make_average_subject



On 3/17/2021 8:36 PM, Jordan Mullins wrote:

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Yes, I had seen that report and had downloaded the patch, but still got the same error. Are there any other steps I can take?

On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
This problem is documented (along with a fix) on our release notes
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On 3/16/2021 3:39 PM, Jordan Mullins wrote:

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Yes, I used the make_average_subject command. I've attached a text file below of the command line and terminal output from my attempt to average two subjects. I get the same error when I try this with the full sample.

On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
What command are you using? make_average_subject? Send the command line and terminal output

On 3/10/2021 3:53 PM, Jordan Mullins wrote:

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Hello,

I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open file". I've read that several others have solved this issue by installing the patch available at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/. I did this, but continue to get the same error. I'm working with Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the recon-all.log below, but please let me know if you need additional information.

Any insight on this would be appreciated! Thank you!

Jordan

--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside


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--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside


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--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside


_______________________________________________
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--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside



--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside


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--
Jordan L. Mullins, B.A.
Doctoral Student, Department of Psychology
University of California, Riverside
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