Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

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Hello,

I checked and my sources.sh is located in /opt/freesurfer-6.0.0/freesurfer/sources.sh not /opt/freesurfer-6.0.0/sources.sh. I opened the kvlAutoCropt file and it found this source $FREESURFER_HOME/sources.sh kvlAutoCrop.bin "$@" Can I edit the kvlAutoCrop file to point the correct? or something else

Best, Miracle

On Wed, May 30, 2018 at 11:55 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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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)

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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.uk> wrote:

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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.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 16:11 *To: *Douglas N Greve freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0)

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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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