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:
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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 ru
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Hi again,
Just wanted to confirm the randomness of the issue… and see if there was any
potential explanation for this.
I decided to go back from scratch, using a copy of my scans processed with
FS5.3.
I re-ran the thalamic nuclei pipeline from FS7.2
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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 64
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It’s possible something in 7.2.0 still requires MCRv84. If so, it is
probably not going to work to use a soft link to fake out the name, and using a
different version of Matlab run time could explain the crashes.. Please
send along the output showi
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Interesting… when I leave the folders named MCRv93 or MCRv97 (one at a time,
not present together at the same time), then FS tells me I need to install
MCRv84!
FS7.2.0 seems to only recognise MCRv84, hence why I used for example, sudo ln
-s v93 MCRv8
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After you install either R2017b or R2019b using the fs_install_mcr script you
should end up with either ./freesurfer/MCRv9.3 or ./freesurfer/MCRv9.7
There are no soft links to create manually and there should be no references to
MCRv8.4 in DYLD_LIB
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Thanks again for your help.
I tried with both R2017b and R2019b but no luck.
When I soft link either of these versions to MCRv84, I receive the following
error:
sub-BA_IGP001
Setting ITK threads to 1
#
#@#
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One error in the logs is from missing symbols in the Matlab java library, and
another says to contact the Mathworks for technical support. But
Mathworks is not going to support you because MacOS 10.13 does not meet the
system requirements for R2014b
External Email - Use CautionThanks for your help!I followed your instructions, but still have these issues.Actually, it seems to happen quite randomly, as I could process some subjects but not other, and also on subjects that I could previously process (I am using a loop for several
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MCRv84 looks like it should run on MacOS 10.13, so in a new terminal window, I
would install it directly into the freesurfer distribution with,
$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0$ cd $FREESURFER_HOME$
rm -rf MCRv84
$ cd bin
$ su
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Hi all,
Just bumping this one up.
Any help would be really appreciated.
Thanks in advance,
Yann
> On 27 Aug 2022, at 10:47 am, Yann Quidé wrote:
>
> Hi team,
>
> I have been having troubles with processing my scans for thalamic subnuclei.
> In my
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Hi team,
I have been having troubles with processing my scans for thalamic subnuclei.
In my previous post, I mentioned I was using FS7.3.2, but indeed realised that
this version was not fully compatible with my OS (OSX 10.13). So I instead
installed
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Not a good news for me, but thanks!
Yann
> On 20 Aug 2022, at 06:40, fsbuild wrote:
>
> Hello Yann,
>
> It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on
> your machine running MacOS (10.13) to work with the Matlab MCRv97
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Hello Yann,
It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on
your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime
environment. MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer
supported by Ap
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Hi team,
I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans
processed with recon-all from FS5.3 (mac OSX10.13).
However, I receive the below error.
Any idea how I could solve this?
Thanks in advance.
Yann
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