External Email - Use Caution
Sorry, I meant pwd, dirname, etc
-- 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 17:16 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
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.ukmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jasmin Alves <jalves@usc.edumailto:jalves@usc.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 11 July 2018 at 16:26 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:jalves@usc.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edumailto:jalves@usc.edu