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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 < e.igles...@ucl.ac.uk> 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/ > 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> 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> on behalf of miracle > ozzoude <miracoo...@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) > > > > * 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> 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> on behalf of miracle > ozzoude <miracoo...@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.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> on behalf of miracle > ozzoude <miracoo...@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 > > > _______________________________________________ > 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. > > > > > _______________________________________________ > 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. > > > > > _______________________________________________ > 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. > > > > _______________________________________________ > 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. > >
_______________________________________________ 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.
