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> 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> 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


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