External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu> on behalf of Jasmin Alves <jal...@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. 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. 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 jal...@usc.edu<mailto:jal...@usc.edu>
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