Hi Shahrazd

can you try:

chmod -R a+rx  $FREESURFER_HOME/bin

and see if that fixes your problem?


On Mon, 9 Sep 2019, shahrzad kharabian wrote:

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I have already run recon-all with default options on a large set of
T1-weighted images, using Freesurfer v 6.0. 
Now we want to extract the hippocmpal subfields from these already processed
Apparently our installation was missing Matlab Compiler Runtime (MCR) for
Matlab 2012b.
We followed the instructions and downloaded it and placed it in the

Yet now when running the "recon-all -s subj_id -hippocampal-subfields-T1"
command, I get the following error:

$FREESURFER_HOME/bin: Permission denied.

and the error occurs in the step:


I am using a bash shell. But also temporarily changing the shell to tcsh and
adding the Freesurfer to the path, did not solve the problem. 

How can the error be avoided?

Thanks a lot for your help in advance,

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