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
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-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
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:
External Email - Use CautionHi 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.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
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.
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-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.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
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.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHey 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
*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:
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
*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
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.
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-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)
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.iglesias@ucl.ac.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.
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.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionNo, 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.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)
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.iglesias@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
*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:
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
*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
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.
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-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 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.iglesias@ucl.ac.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 17:39
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.iglesias@ucl.ac.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:e.iglesias@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto: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.
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 < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHi 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
*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 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.iglesias@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
*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)
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.iglesias@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
*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:
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
*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
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.
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
________________________________ 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/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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 18:57
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 17:39
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.
External Email - Use Caution
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 < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHard 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
*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 CautionThanks.
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.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHi 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.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 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.iglesias@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
*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)
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.iglesias@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/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.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:
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
*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
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.
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 miracooloz@gmail.com 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 < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHard 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
*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 CautionThanks.
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.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionHi 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.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 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.iglesias@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
*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)
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.iglesias@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/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.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:
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
*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
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.
External Email - Use Caution
Hi again,
the binaries are under $FREESURFER_HOME/bin, in your case, /opt/freesurfer-6.0.0/bin.
After sourcing FreeSurfer, is /opt/freesurfer-6.0.0/bin in your path? If it is, I can't understand why the code wouldn't find the executables...
Cheers,
/Eugenio
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: Thursday, May 31, 2018 8:37:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
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 <miracooloz@gmail.commailto:miracooloz@gmail.com> 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 <e.iglesias@ucl.ac.ukmailto: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/freesurfer-6.0.0/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
recon-all .......
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto: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/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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 18:57
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 17:39
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.iglesias@ucl.ac.ukmailto:e.iglesias@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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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/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.ukmailto: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
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Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto: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.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.
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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.
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Iglesias Gonzalez, Eugenio -
miracle ozzoude