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Hello,

I am trying to run trac-all -bedp and I am running into the following error:

/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

Others have encountered this error previously, and you had advised running bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if there is a way to still run bedpostx inside trac-all.

I was looking at the source code for trac-all in your github (branch 7.2), and I noticed that line 611 calls bedpostx_mgh despite being within the "if (! $onpbs)" conditional. Would changing line 611 from:

set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)

set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem?

If it's helpful:

I am running on centos7 and my build stamp is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks,

Amy

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