External Email - Use Caution
Dear Freesurfer Experts,
I ran the following command in FS:
recon-all -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/SW1-1875_M12/Brain/DICOM/0000D7EA/AACF54F0/AAA4DDA4/000037CC/EE021428 -subject 000037CC -qcache -hippocampal-subfields-T1 -brainstem-structures -cw256 -3T -all
The command exited with error. Attached the log file.
Additionally, this message shows up in the terminal output:
ERROR: cannot find Matlab 2012b runtime in location:
/Applications/freesurfer/MCRv80
It is looking for either:
bin/glnxa64/libdctprocess.so (Linux 64b) or
bin/maci64/libdctprocess.jnilib (Mac 64b)
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b.
To do so, please run the following commands (you might need root permissions):
LINUX:
cd /Applications/freesurfer
curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz"
tar xvf runtime2012b.tar.gz
MAC:
cd /Applications/freesurfer
curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz"
tar xvf runtime2012b.tar.gz
I did now download the runtime2012b according to the suggestion. The untaring created a folder called MCRv80. I moved this folder to the Freesurfer_Home.
Before I run everything again: 1.) Is the correct procedure to download the Matlab runtime? 2.) Did the recon-all run everything just without hippocampal subfields and brainstem? If yes, can I just re-run these two commands or do I need to re-run everything?
Many thanks for the support!
/Ben
____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01