You can also try segment_subregions. This is a python implementation
that gives almost exactly the same result (but limited to T2). See
https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation
It should run on Mac
On 8/31/2022 11:28 PM, fsbuild wrote:
External Email - Use Caution
For MacOS, the 7.2.0 release was done on MacOS 10.14.6 and it will
check for Matlab runtime MCRv84 which you install with R2014b as the
argument to fs_install_mcr
For MacOS, the 7.3.2 release was done on MacOS 10.15.7 and it will
check for Matlab runtime MCRv97 which you install with R2019b as the
argument to fs_install_mcr
I think we already know your machine running MacOS 10.13 does not
match the above but MCRv84 sometimes works for you running the 7.2.0
release. The errors you posted from Matlab could be an issue with
MCRv84 w.r.t MacOS 10.13 or your machine. Upgrading your OS to match
the above could eliminate the matlab errors.
If you want to experiment with running different versions of Matlab,
e.g., R2017b, then you can go into the file
./freesurfer/bin/checkMCR.sh and comment out the check for the version
of matlab by adding pound sign “#” to the beginning of the lines that
do the check. Then you don’t need to try and bypass the check with
soft links. But we have not done testing for the above releases on
MacOS 10.13.
I don’t know if you have experience with using multiple boot
partitions for MacOS (set via Startup Disk in System Prefeernces).
One test would be to do a clean install of MacOS 10.14 or 10.15 on an
empty (internal) disk partition or external disk drive. Then boot
from that partition and install the 7.2.0 or 7.3.2 release with the
matching version of Matlab listed above. You would probably want at
least a USB3 connection (or equivalent speed) to an external drive for
that to not run slowly. A clean install should eliminate any issues
with the current state of your machine. Then try running your
commands with the matching Freesurfer release in the new/clean version
of the OS.
- R.
On 31 Aug 2022, at 2:12 pm, Yann Quidé <yannqu...@gmail.com> wrote:
This is the error I get when for example, I use MCRv93
sub-BA_IGP001
ERROR: cannot find Matlab 2014b runtime in location:
/Applications/freesurfer/7.2.0/MCRv84
It is looking for either:
bin/glnxa64/libmwlaunchermain.so (Linux 64b) or
bin/maci64/libmwlaunchermain.dylib (Mac 64b)
The hippocampal/amygdala and brainstem modules require the (free)
Matlab runtime.
You will need to download the Matlab Compiler Runtime (MCR) for
Matlab 2014b.
To do so, please run the following command (you might need root
permissions):
fs_install_mcr R2014b
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
