Hello Ducan,
Thanks I had changed FSL_DIR to FSLDIR as you suggested
Now FSL 5.0 is succesfully installed If I write fsl in terminal FSL5.0 GUI opens without error. with no problem in fslview also
I am having specific problems in running certain scripts like fslmaths,cluster, fast please see below
mv@mv-HP-Z210-Workstation:~$ fast
fast: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
mv@mv-HP-Z210-Workstation:~$ fslmaths
fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
mv@mv-HP-Z210-Workstation:~$ cluster
cluster: error while loading shared libraries: libutils.so: cannot open shared object file: No such file or directory
while scripts like atlasquery and few others are working fine
I doubt thefollowing might br the problem:-
I am using bash (shell script) and there is no mention about FSL_DIR in whole script and my .bashrc file also don't have any line like /usr/share/fsl/4.1/bin. So why I am getting the warning WARNING: /usr/share/fsl/4.1/bin does not exist. (see below)
I am getting this warning after reinstalling FSL 4.1 in the initial opening of termiinal. Can you mention the reason why?
-------- freesurfer-Linux-centos4-stable-pub-v5.1.0 --------
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
WARNING: /usr/share/fsl/4.1/bin does not exist.
FSL_DIR /usr/share/fsl/4.1