When I look at the README, this is the contents. Are you looking at
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/README ?
Download make_average_subject and the platform-specific version of
mri_aparc2aseg
from this directory and move them to your freesurfer bin directory via:
mv make_average_subject $FREESURFER_HOME/bin
mv mri_aparc2aseg.platform $FREESURFER_HOME/bin/mri_aparc2aseg
chmod +x $FREESURFER_HOME/bin/mri_aparc2aseg
$FREESURFER_HOME/bin/make_average_subject
We currently do not have a mac build of mri_aparc2aseg, and we recommend
downloading the freesurfer dev release to resolve this issue.
On 4/6/2021 6:29 PM, Jordan Mullins wrote:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu <mailto:dgr...@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:
External Email - Use Caution
Hi Douglas,
Just following up on this. Thanks!
On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins
<jordan.mull...@email.ucr.edu
<mailto:jordan.mull...@email.ucr.edu>> wrote:
Yes! Results attached.
On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@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:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu <mailto:dgr...@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:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu
<mailto:dgr...@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:
External Email - Use Caution
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
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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.*
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University of California, Riverside
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*Jordan L. Mullins, B.A.*
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University of California, Riverside
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*Jordan L. Mullins, B.A.*
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*Jordan L. Mullins, B.A.*
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*Jordan L. Mullins, B.A.*
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