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
