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.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

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.

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

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.edumailto: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.