If there really is a .license in the FREESURFER_HOME directory then everything should be working fine. What is the output when you type:
'ls -l /Applications/freesurfer/.license' at the command line? And what is the output when you type: 'ls -l $FREESURFER_HOME/.license' On 10/24/2013 11:25 AM, muellersvenc wrote: > Hi Zeke, > > that seems to have worked (strangely because I didn't really do anything > different before other than a fresh reinstall). > > However, now I have problems with the license file when trying to test the > installation as suggested on the "Testing your freesurfer installation" > webpage. > > I did a fresh installation, then created a ".license" file using the text > editor containing the three lines that were sent to me by email and placed > this file into the freesurfer folder which is my FREESURFER_HOME > (/Applications/freesurfer). Then I did the sourcing. And then when I type for > instance > > [pp05c332:/Applications] switch% tkmedit bert orig.mgz > -------------------------------------------------------------------------- > ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -------------------------------------------------------------------------- > [pp05c332:/Applications] switch% > > > Any ideas what I am doing wrong? I changed the settings on my computer a > while ago and I can see the hidden files so can also see that there is a file > called ".license" in the freesurfer folder but am not sure why freesurfer is > not recognising it. > > Many thanks in advance for your help! > > sven > > > > On 24-okt-2013, at 16:39, Z K wrote: > >> Hi Sven, >> >> Whats most likely happening is that you are defining SUBJECTS_DIR prior to >> sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the SUBJECTS_DIR >> environment variable if it already exists at the time of sourcing the >> SetUpFreeSurfer.csh. This is most likely occuring in your .cshrc file. >> >> To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the output >> says. >> >> -Zeke >> >> On 10/24/2013 09:10 AM, muellersvenc wrote: >>> Hi all, >>> >>> I am running into trouble testing my freesurfer installation on a Mac >>> (10.6.8). I followed all steps in the guide but there is something funny >>> that freesurfer does not seem to recognise its own "subjects" directory >>> (see attached screenshot). If screenshot is not visible, it says: >>> >>> -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> WARNING: Applications/freesurfer/subjects does not exist >>> FREESURFER_HOME /Applications/freesurfer >>> FSFAST_HOME /Applications/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR Applications/freesurfer/subjects >>> MNI_DIR /Applications/freesurfer/mni >>> FSL_DIR /usr/local/fsl >>> >>> I think it might have to do with the fact that there is a "/" missing in >>> front of the "Applications" but I don't know where/how to change this. I >>> checked my StartUp.csh file and there everything seems fine. However, the >>> subjects directory was definitely created by freesurfer (also screenshot) >>> so there is a mismatch somewhere. >>> >>> I am sure it is a simple thing but can someone please let me know what I >>> should do so I can start to enjoy freesurfer? >>> >>> Many thanks in advance, >>> >>> sven >>> >>> >>> >>> >>> _______________________________________________ >>> 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
