External Email - Use Caution
Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is inaccessible. Recon-all works great.
Thanks, Jasmin On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionDear 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
*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.
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
jalves@usc.edu
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