External Email - Use Caution
Hello Eugenio,
I noticed Matlab doesn't open when I run the hippocampal analysis, so when I tried to click on the file, segmentSubjectT1_autoEstimateAlveusML,
I encountered the following error:
Check with the developer to make sure segmentSubjectT1_autoEstimateAlveusML works with this version of OS X. You may need to reinstall the application. Be sure to install any available updates for the application and OS X.
Thanks, Jasmin
On Wed, Jul 11, 2018 at 9:15 AM, Jasmin Alves jalves@usc.edu wrote:
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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-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu