I must be really cpu challenged because I can't even seem to get this thing started. I am trying to perform basic set up right now. I have downloaded freesurfer so far and in the freesurfer setup and configuration section of the wiki I have been able to
If using bash or sh, type:
export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I do have this come up in the window.
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
Now this is where my problems start I would like to do this but I do not see any of these files anywhere. I am using bash but I do not see the corresponding .bashrc file anywhere to include the export and source commands.
Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script).
Also I am having trouble with the license step.I tried making the .license file and pasting my information in as well as trying the ways suggested in previous peoples problems (using pico). I guess I am having a problem understanding where my $FREESURFER_HOME is located to put my .lisence file.
I am still fresh to using the unix terminal so I apologize if my problem is due to my inexperience but if you could help me out I would really appreciate it.
Thank you
Try this: cd ~ vi .bashrc
You wont see the .bashrc unless you use ls -a
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business
2009/9/22 Weisinger, Brian (NIH/OD) [E] Brian.Weisinger@nih.gov
I must be really cpu challenged because I can't even seem to get this thing started. I am trying to perform basic set up right now. I have downloaded freesurfer so far and in the freesurfer setup and configuration section of the wiki I have been able to
If using bash or sh, type:
export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I do have this come up in the window.
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
Now this is where my problems start I would like to do this but I do not see any of these files anywhere. I am using bash but I do not see the corresponding .bashrc file anywhere to include the export and source commands.
Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script).
Also I am having trouble with the license step.I tried making the .license file and pasting my information in as well as trying the ways suggested in previous peoples problems (using pico). I guess I am having a problem understanding where my $FREESURFER_HOME is located to put my .lisence file.
I am still fresh to using the unix terminal so I apologize if my problem is due to my inexperience but if you could help me out I would really appreciate it.
Thank you
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Pedro Paulo de Magalhães Oliveira Junior -
Weisinger, Brian (NIH/OD) [E]