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Hi Andrew,

Thank you for your reply, I really appreciate it. Sudo would not allow, so instead I downloaded MATLAB separately and attempted to follow that protocol. I managed to get quite far into the SegmentThalamicNuclei.sh process, but have reached the following error message;

Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information (/Applications/freesurfer/7.1.1/subjects/subject01/tmp/THnuclei_v12_useTwoComponents_1_T1/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Caught unexpected exception of unknown type.

------------------------------------------------------------------------
       Segmentation violation detected at Tue Mar 23 09:06:57 2021
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Current Visual     : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root        : /Applications/MATLAB_R2014b.app
  MATLAB Version     : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.2.0 Darwin Kernel Version 20.2.0: Wed Dec  2 20:40:21 PST 2020; root:xnu-7195.60.75~1/RELEASE_ARM64_T8101 x86_64
  Processor ID       : x86 Family 6 Model 44 Stepping 0, GenuineIntel
  Software OpenGL    : 0
  Virtual Machine    : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
  Window System      : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

I’m wondering if I could please once again ask for your expertise - does this fault look familiar? 

Kindest regards,
Matt
On 16 Mar 2021, at 19:59, Hoopes, Andrew <AHOOPES@MGH.HARVARD.EDU> wrote:

Hi Matt,
 
Hopefully this isn’t specific to M1, but I’m not sure it would be in this case. Maybe try running fs_install_mcr with sudo in front? Some users are suggesting it here:
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best
Andrew
 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Cleary, Matthew <M.Cleary2@liverpool.ac.uk>
Date: Friday, March 12, 2021 at 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Matlab Runtime error line 334

        External Email - Use Caution        

Hi team,

I’m wondering if I could please ask for help - I am trying to install fs_install_mcr R2014b on a 2020 M1 chip MacBook. I’m encountering an error at the end, that goes as follows;

inflating: sys/java/jre/maci64/jre/THIRDPARTYLICENSEREADME.txt
  inflating: sys/java/jre/maci64/jre/Welcome.html
  inflating: trademarks.txt
./install: line 334: /var/folders/2f/fyngt3b52mn39mcc6_419q8h0000gn/T/tmp.rt0pgVdq/bin/unknown/install_unix: No such file or directory
ls: /var/folders/2f/fyngt3b52mn39mcc6_419q8h0000gn/T/tmp.rt0pgVdq/install-target/v*: No such file or directory

Do you have any idea how I can fix this? Any help would be massively appreciated.

Kindest regards,
Matt

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