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Hello,I was able to solve the previous error (not finding the sources.sh) however, i have encountered another error (please find the attached hippocampal-subfileds-T1.log file). In this case, line 3 of kvlAutoCrop has a problem with kvlAutoCrop.bin....Thanks,Best,MiracleOn Wed, May 30, 2018 at 6:03 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:External Email - Use Caution
Hard to tell without seeing the contents of the directories, but I'd put my money on:
export FREESURFER_HOME=/opt/freesurfe
r-6.0.0/freesurfer source $FREESURFER_HOME/SetUpFreeSurf
er.sh recon-all .......
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of miracle ozzoude <miracooloz@gmail.com>
Sent: Wednesday, May 30, 2018 9:21:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)External Email - Use Caution
Thanks.
So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source $FREESURFER_HOME/freesurfer/Se tUpFreeSurfer.sh" (based on printenv). However, when i tried to run my script i got another error (/opt/freesurfer-6.0.0/freesur fer/SetUpFreeSurfer.sh: line 42: /opt/freesurfer-6.0.0/FreeSurf erEnv.sh: No such file or directory). This is line 42 "source $FREESURFER_HOME/FreeSurferEnv .sh".
Do you think it's wise if i add another line (line 43) with the command "source $FREESURFER_HOME/freesurfer/FreeSurferEnv.sh" and comment line 42? It might solve the problem.
Best,Miracle
On Wed, May 30, 2018 at 2:43 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:
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Hi again,
The two following statements are inconsistent! I believe that’s the root of the problem:
a. When i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
b. I always insert this lines " export FREESURFER_HOME=/opt/freesurfe
r-6.0.0/freesurfer
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.ha
rvard.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 18:57
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
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Yes, because I processed all my subjects with v6.0 without any issue. When i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
I always insert this lines " export FREESURFER_HOME=/opt/freesurfe
r-6.0.0/freesurfer; source $FREESURFER_HOME/SetUpFreeSurf er.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
From: <freesurfer-bounces@nmr.mgh.ha
rvard.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/freesurf
er/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/freesurf
er/ Please double check.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.ha
rvard.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/freesurfe
r-6.0.0/freesurfer; source $FREESURFER_HOME/SetUpFreeSurf er.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
From: <freesurfer-bounces@nmr.mgh.ha
rvard.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.harvar
d.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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