Hi,
I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2). Any help would be appreciated. Basically, when trying example 2 in instructions homepage I got the following error:
theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all
bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory
But the fact is that recon-all is there and apparently it is well configured, because 1) the recon-all does exist, and 2) permissions are ok:
theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all
-rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 /usr/local/freesurfer/bin/recon-all
and the command is promptly recognized :
theo@theo-Inspiron-5457:~$ which recon-all
/usr/local/freesurfer/bin/recon-all/
Any ideas? Anybody got this issue before? It seems to be some (not obvious) permission problem.
Below I type the whole procedure to install, so one can see that I followed all installation instructions.
History:
1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer
2) Successful set up of environment variables after including the following lines in .bashrc:
##############################################
#Software FREESURFER - Enviroment variables
#
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/home/theo/freesurfer/subjects
##############################################
BTW, "theo" is my userID
3) File license.txt copied to /usr/local/freesurfer
4) message after open a terminal window confirms that Enviroment variables were correctly set:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
(base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR
/home/theo/freesurfer/subjects
(base) theo@theo-Inspiron-5457:~$
Any help is welcome
Regards
Theotonio