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 <jal...@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.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> on behalf of Jasmin >> Alves <jal...@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 >> >> jal...@usc.edu >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm >> r.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=clK >> 7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rN >> RHLug&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.part >> ners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BO >> UHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=w4MGsgIqoYbSnH >> HZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8&s=2mrR0Thpt73B1ran6vJjkbnFjoZ7 >> wovDcNc23JUxZLY&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 > > -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jal...@usc.edu
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