I forgot to mention, if you do install the complete FSL package, you can use that one with Freesurfer by doing the following:

cd $FREESURFER_HOME rm -Rf fsl ln -s /path/to/my/fsl fsl

where /path/to/my/fsl is where you install FSL.

On Wed, 2007-10-10 at 14:13 -0400, Nick Schmansky wrote:

Zonglei Zhen,

The FSL included with Freesurfer is not a complete installation of FSL.

You can get the complete FSL installation here:

http://www.fmrib.ox.ac.uk/fsldownloads/

Nick

On Wed, 2007-10-10 at 15:02 +0800, Zhen Zonglei wrote:

...

Hi all: I have installed fsl with freesurfer 4.0.1, but some errors were reported when I run fsl:

...

source new_fs.csh

Setting up Enviroment for NewFreeSurfer && new_subjects -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /nfs/h1/r1/new_soft_test/freesurfer FSFAST_HOME /nfs/h1/r1/new_soft_test/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /nfs/h1/r1/new_soft_test/freesurfer/subjects MNI_DIR /nfs/h1/r1/new_soft_test/freesurfer/mni FSL_DIR /nfs/h1/r1/new_soft_test/freesurfer/fsl

...

fsl

/nfs/h1/r1//new_soft_test/freesurfer/fsl/bin/fslwish: line 17: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: No such file or directory /nfs/h1/r1/new_soft_test/freesurfer/fsl/bin/fslwish: line 17: exec: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: cannot execute: No such file or directory

Can someone give some cues how to slove this problem?

Thanks

Zonglei Zhen

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