Dear Jasmin,

The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path?

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jasmin Alves <jalves@usc.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 11 July 2018 at 16:26
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields".
However, several errors come up when I run:

recon-all -s 102 -hippocampal-subfields-T1

#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018

dirname: Command not found.

pwd: Command not found.

/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

#--------------------------------------------

#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018

dirname: Command not found.

pwd: Command not found.

/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

I have searched through the list to see if anyone else has had this issue but to no avail.

Version:

freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

OS: X V 10.9.5

Thanks!

Jasmin

Jasmin Alves

Doctoral Candidate

Medical Biology Graduate Program

University of Southern California

jalves@usc.edu