External Email - Use Caution
Hey so kvlAutoCrop is looking for sources.sh in /opt/freesurfer-6.0.0/ which seems to be FREESURFER_HOME at that point. However, from the rest of your code, it seems that FREESURFER_HOME is /opt/freesurfer-6.0.0/freesurfer/ Please double check. Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of miracle ozzoude miracooloz@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
External Email - Use Caution Hello Eugenio,
Thanks for the response. All my processing was done with FreeSurfer v6.0 although, we have version 5.3 installed on the server too. I always set my environment to version 6 ( export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.sh) before running any processing.
Also, our server has matlab2008b installed but, it expired hence, i don't think that will interfere with the processing because we installed the correct/recent matlab runtime.
Best, Miracle
On Wed, May 30, 2018 at 11:35 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:
External Email - Use Caution Hi Miracle, I believe Doug (CCed) ran into a similar problem recently, and I think the problem had to do with mixing versions. What exact version are you using? Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
External Email - Use Caution Hello,
I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link (https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it was installed on the same server as v6.0). The installation process worked fine.
However, when I wanted to run recon-all on already processed FS data ( e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1 -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I have attached the log for your viewing. Thank you.
Best, Miracle
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