Hi Hannah,



What kind of environment are you running this in? These errors make it seem like you do not have a PATH variable set at all. Are you using bash? and what operating system?



best

Andrew





> On Jan 22, 2018, at 4:06 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

>

> Hi Hannah,

> This seems like a more general problem with your PATH, but I’m sure Andrew (CCed) has a better idea of what might be going on.

> Cheers,

> /Eugenio

>

> --

> Juan Eugenio Iglesias

> ERC Senior Research Fellow

> Translational Imaging Group

> University College London

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>

>

> On 20/01/2018, 00:23, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hannah's USC Email" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of shanluo@usc.edu> wrote:

>

>

>    Hi Freesurfer experts,

>

>    I tried to do hippocampus subfield analysis but failed. I got this error message:

>

>    #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 15:27:36 PST 2018

>    dirname: Command not found.

>    pwd: Command not found.

>    pwd: Command not found.

>    /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

>    #--------------------------------------------

>    #@# Hippocampal Subfields processing (T1 only) right Fri Jan 19 15:27:36 PST 2018

>    dirname: Command not found.

>    pwd: Command not found.

>    pwd: Command not found.

>    /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

>

>    Your help would be greatly appreciated. Thanks!

>

>

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