External Email - Use Caution 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/freesurfer-6.0.0/freesurfer Cheers, /E -- 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-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracoo...@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) External Email - Use Caution 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/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.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of miracle ozzoude <miracoo...@gmail.com<mailto:miracoo...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 30 May 2018 at 17:39 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution 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.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of miracle ozzoude <miracoo...@gmail.com<mailto:miracoo...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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.igles...@ucl.ac.uk<mailto:e.igles...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of miracle ozzoude <miracoo...@gmail.com<mailto:miracoo...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu<mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
