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.
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@nmr.mgh.harvard.edu
-
muellersvenc -
Z K