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-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 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.igles...@ucl.ac.uk<mailto:e.igles...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Jasmin Alves <jal...@usc.edu<mailto:jal...@usc.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 11 July 2018 at 16:26 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=JWFtZN0TxhbF-szDNVVAGtRlTVerKBV7GCF0cFlu-_w&e= 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_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY&e= . 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 jal...@usc.edu<mailto:jal...@usc.edu>
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