This errer message mean that you are missing /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh in your /usr/share/fsl/5.0/etc/fslconf. You should get a copy of this file and place in /usr/share/fsl/5.0/etc/fslconf/f

knut J

On 10/09/2012 02:00 PM, David Soto wrote:

hi - so the output to source $FREESURFER_HOME/SetUpFreeSurfer.csh

was:

...

...

-------- freesurfer-Linux-centos4_x86_64-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
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found.
FSL_DIR           /usr/share/fsl/5.0

On Tue, Oct 9, 2012 at 11:54 AM, Knut J Bjuland <knutjbj@hotmail.com mailto:knutjbj@hotmail.com> wrote:

Can you please send me the output again?  The files should not
prevent you from starting since fsl and freesurfer need that file
to be able to set the environment right.


On 10/09/2012 10:41 AM, David Soto wrote:

...

thanks, I'll try though I have already reinstalled
FSL now I have FSL 5.0.1- should that fine prevent
FS from starting up anyway?
Cheers

On Tue, Oct 9, 2012 at 9:06 AM, Knut J Bjuland
<knutjbj@hotmail.com <mailto:knutjbj@hotmail.com>> wrote:

    Hi

    You should reinstall FSL 5.0 since it is missing a file.

    Knut J



    On 10/08/2012 08:05 PM, David Soto wrote:

...

    Hi, just trying to install Fresufer in Ubuntu OneiricOcelot
    11.10,

    I followed the installation steps in your web and seemed fine

     in one of the last steps I did

    wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh
    -------- freesurfer-Linux-centos4_x86_64-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
    /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not
    found.
    FSL_DIR /usr/share/fsl/5.0


    the thing is that when I test the install by typing

    tkmedit

    it says command not found & cannot get Freesurfer to start

    can you help please?

    Thanks!

    David
    http://www1.imperial.ac.uk/medicine/people/d.soto/


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