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/

I always insert this lines " export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for freesurfer. 

Best, 

Miracle 

On Wed, May 30, 2018 at 12:47 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

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No, the contents of kvlAutoCrop are what they should be. What I don’t understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh  (this is what your log says). Are you sure FREESURFER_HOME is properly defined?

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 17:39

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: 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)

 

        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.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)

 

        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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.