That’s weird. What is the output of the following command? ls /path/to/my/subjects/freesurferfolder
And of this one: ls /path/to/my/subjects/freesurferfolder/SUBJECT/mri/lh.hippoSfVolumes*.txt (where SUBJECT is a subject of your choice) Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 17:04, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi Eugenio, That's actually the issue, it doesn't generate any file at all.. there's no hippo.txt in the folder where I run it, or in the subject's directory that I had specified. Batool ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command Hi Batool What are the contents of hippo.txt? Just empty? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com<http://www.jeiglesias.com/> http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 16:41, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder of the subjects (used *'s here for subjects and their freesurfer folder), but it still gives no output. It just says: Gathering results from subjects in: /path/to/my/subjects/freesurferfolder Using the suffix name: T1 And writing them to: hippo.txt What am I doing wrong here? Thanks so much! Batool _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
