Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, Thanks for your email. We have identified the problem an it will be fixed for the next build of our development version. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Cc: e iglesias e.igles...@bcbl.eu Sent: Thursday, August 20, 2015 2:29:16 PM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Ah, I see. This issue must have arisen due to some changes I made in the freesurfer git repository. Eugenio, I should have this resolved by tomorrows build. Alexandra, thanks for pointing this out. It should be fixed in tomorrows daily build. Ill send you an email to confirm. -Zeke Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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.
