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Hello Elizabeth,

I don’t see anything wrong with how the 6.0.4/bin/bet2 binary is built.

It would be interesting to see if the output is different with an older fsl version like 5.0.7.

In a new/different terminal window you could setup your environment with 5.0.7 and then try again,

$ setenv FSLDIR /usr/pubsw/packages/fsl/5.0.7
$ setenv FSL_DIR "$FSLDIR"

.  .  . then source freesurfer setup or run .  .  .

$ source $FSLDIR/etc/fslconf/fsl.csh

- R.

On Dec 27, 2021, at 15:34, Kaplan, Elizabeth <elizabeth_kaplan@brown.edu> wrote:

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Hello All, 

I am running into an error when attempting to run the 'trac-all -prep -c" command. The error reads "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4/bin/bet: line 399:  6625 Illegal instruction"

I set my FSLDIR following the instructions on the FSL User guide and added these lines to my .bash_profile file. 

Any suggestions on how to navigate this issue? Thank you in advance!

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