Hi Eugenio, Here are my outputs:
ls e009723_FS (one of my subject's freesurfer folder):
bem FS1.sh FS2.sh FS4.sh label mri scripts src stats surf tmp touch trash
- you can ignore the FS#.sh files - these are matlab script files we run.
ls mri/lh.hippoSfVolumes*.txt:
mri/lh.hippoSfVolumes-T1.v10.txt
Thanks! Batool ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Monday, February 13, 2017 1:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command
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 <br2499@cumc.columbia.edumailto:br2499@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.ukmailto:e.iglesias@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.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/
On 13 Feb 2017, at 16:41, Rizvi, Batool <br2499@cumc.columbia.edumailto:br2499@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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