Hi Zeke, that did the trick!!
Thanks so much for your help! sven On 24-okt-2013, at 21:40, Z K wrote: > Sven, > > Well that certainly is odd that. My guess is that there is some sort of > extension that Mac is hiding in the finder window (along the lines of what > you were talking about with the text editor). > > Im also a little concerned about the double '//' that is part of your > FREESURFER_HOME environment variable. That should not be there, although I > don't think its necessarily a problem. > > Please open a terminal and type the following command: > > 'touch /Applications/freesurfer/.license' > > That should fix your problem. Let me know if not. Also, please CC the list on > these responses so that they can be stored for others to view. > > -Zeke > > > On 10/24/2013 02:29 PM, muellersvenc wrote: >> Hi Zeke, >> >> the output in both cases is: "no such file or directory". I have attached a >> screenshot to this email and you can see my freesurfer directory and the >> .license file at the very top. Is this maybe a problem with creating such a >> file with the text editor? There is also a file called LICENSE in the >> directory but this just contains the license agreement. >> >> I really appreciate you helping me as I am keen on getting freesurfer to >> work. So, thank you so much for your time and effort in helping me through >> this! Much appreciated! >> >> Sven >> >> >> >> >> >> On 24-okt-2013, at 17:35, Z K wrote: >> >>> 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
