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 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-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


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--
Jasmin Alves
Doctoral Candidate 
Medical Biology Graduate Program 
University of Southern California



--
Jasmin Alves
Doctoral Candidate 
Medical Biology Graduate Program 
University of Southern California