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.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.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [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.com
http://cmictig.cs.ucl.ac.uk/


On 13 Feb 2017, at 16:41, Rizvi, Batool <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 
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