External Email - Use Caution My freesurfer home is /opt/freesurfer-6.0.0 which contains all the necessary freesurfer binaries, .sh files etc in order for freesurfer to run. I always include this in my shell script export FREESURFER_HOME=/opt/freesurfer-6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh
On Thu, May 31, 2018 at 3:33 PM, miracle ozzoude <[email protected]> wrote: > 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, > Miracle > > On Wed, May 30, 2018 at 6:03 PM, Iglesias Gonzalez, Eugenio < > [email protected]> 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/freesurfer-6.0.0/freesurfer >> >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> recon-all ....... >> >> >> Juan Eugenio Iglesias >> >> Centre for Medical Image Computing (CMIC) >> >> University College London >> >> http://www.jeiglesias.com >> >> http://cmictig.cs.ucl.ac.uk/ >> >> >> ------------------------------ >> *From:* [email protected] < >> [email protected]> on behalf of miracle ozzoude < >> [email protected]> >> *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/SetUpFreeSurfer.sh" (based on >> printenv). However, when i tried to run my script i got another error >> (/opt/freesurfer-6.0.0/freesurfer/SetUpFreeSurfer.sh: line 42: >> /opt/freesurfer-6.0.0/FreeSurferEnv.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 < >> [email protected]> wrote: >> >> 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/freesurfe >> r-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: *<[email protected]> on behalf of miracle >> ozzoude <[email protected]> >> *Reply-To: *Freesurfer support list <[email protected]> >> *Date: *Wednesday, 30 May 2018 at 18:57 >> >> *To: *Freesurfer support list <[email protected]> >> *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 < >> [email protected]> 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: *<[email protected]> on behalf of miracle >> ozzoude <[email protected]> >> *Reply-To: *Freesurfer support list <[email protected]> >> *Date: *Wednesday, 30 May 2018 at 17:39 >> >> >> *To: *Freesurfer support list <[email protected]> >> *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 < >> [email protected]> 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/freesurf >> er/ >> >> 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: *<[email protected]> on behalf of miracle >> ozzoude <[email protected]> >> *Reply-To: *Freesurfer support list <[email protected]> >> *Date: *Wednesday, 30 May 2018 at 16:46 >> *To: *Freesurfer support list <[email protected]> >> *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 < >> [email protected]> 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: *<[email protected]> on behalf of miracle >> ozzoude <[email protected]> >> *Reply-To: *Freesurfer support list <[email protected]> >> *Date: *Wednesday, 30 May 2018 at 16:11 >> *To: *Douglas N Greve <[email protected]> >> *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 >> [email protected] >> 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. 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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 >> [email protected] >> 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 >> [email protected] >> 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 >> [email protected] >> 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 [email protected] 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.
