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Hi, 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 images. 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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