Hi again,
The command should be:
quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Nov 2016, at 18:00, Alan Francis <alandarkenergy@gmail.com> wrote:

Hi Eugenio -

The command I used was : 

[afrancis-mac:/Applications/freesurfer/subjects] afrancis% quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

Here are a listing of the files in the mri directory of a given brain:

[afrancis-mac:subjects/DM_130/mri] afrancis% ls -la
total 89392
drwxr-xr-x  47 afrancis  wheel      1598 Nov 16 14:03 .
drwxr-xr-x  13 afrancis  wheel       442 Nov  2 01:48 ..
-rw-rw-r--   1 afrancis  wheel   4938244 Nov 16 02:13 T1.mgz
-rw-rw-r--   1 afrancis  wheel    396646 Nov 16 12:24 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  wheel    428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  wheel    226733 Nov 16 05:49 aseg.auto.mgz
-rw-rw-r--   1 afrancis  wheel      1545 Nov 16 05:18 aseg.auto_noCCseg.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel    226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  wheel    338726 Nov 16 12:26 aseg.mgz
-rw-rw-r--   1 afrancis  wheel    226785 Nov 16 12:21 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  wheel    226733 Nov 16 05:49 aseg.presurf.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.finalsurfs.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.auto.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.mgz
-rw-rw-r--   1 afrancis  wheel    480682 Nov 16 02:46 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  wheel    130178 Nov 16 05:57 filled.mgz
-rw-rw-r--   1 afrancis  wheel     68968 Nov 16 13:31 lh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel     56338 Nov 16 13:31 lh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel       286 Nov 16 13:30 lh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel    109443 Nov 16 12:09 lh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel     17518 Nov 16 02:27 mri_nu_correct.mni.log
-rw-rw-r--   1 afrancis  wheel     14530 Nov 16 02:10 mri_nu_correct.mni.log.bak
-rw-rw-r--   1 afrancis  wheel   1348717 Nov 16 02:46 norm.mgz
-rw-rw-r--   1 afrancis  wheel   3934641 Nov 16 02:27 nu.mgz
-rw-rw-r--   1 afrancis  wheel   2897650 Nov 16 04:50 nu_noneck.mgz
drwxr-xr-x   3 afrancis  wheel       102 Oct 25 11:23 orig
-rw-rw-r--   1 afrancis  wheel   5959814 Nov 16 02:00 orig.mgz
-rw-rw-r--   1 afrancis  wheel   6015638 Nov 16 02:10 orig_nu.mgz
-rw-r--r--   1 afrancis  wheel  10522408 Nov 16 02:00 rawavg.mgz
-rw-rw-r--   1 afrancis  wheel     68830 Nov 16 14:03 rh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel     56219 Nov 16 14:03 rh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel       286 Nov 16 14:03 rh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel    110421 Nov 16 12:09 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel    207344 Nov 16 12:09 ribbon.mgz
-rw-rw-r--   1 afrancis  wheel       119 Nov 16 05:54 segment.dat
-rw-rw-r--   1 afrancis  wheel      1546 Nov 16 03:43 talairach.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel       428 Nov 16 02:44 talairach.log
-rw-rw-r--   1 afrancis  wheel       214 Nov  2 02:25 talairach_with_skull.log
-rw-rw-r--   1 afrancis  wheel       428 Nov 16 05:03 talairach_with_skull_2.log
drwxrwxr-x  14 afrancis  wheel       476 Nov 16 02:10 transforms
-rw-rw-r--   1 afrancis  wheel    377180 Nov 16 05:56 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  wheel    377870 Nov 16 05:56 wm.mgz
-rw-rw-r--   1 afrancis  wheel    422925 Nov 16 05:56 wm.seg.mgz
-rw-rw-r--   1 afrancis  wheel        29 Nov 16 05:54 wm1.txt
-rw-rw-r--   1 afrancis  wheel        29 Nov 16 05:54 wm255.txt
-rw-rw-r--   1 afrancis  wheel    447425 Nov 16 12:36 wmparc.mgz

thanks so much,

Alan

On Tue, Nov 22, 2016 at 12:33 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:
Hi Alan,
Can you please send the the command line that you used to generate the results, and a listing of the files in the mri directory of any subject you’ve analyzed?
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 22 Nov 2016, at 16:48, Alan Francis <alandarkenergy@gmail.com> wrote:

Hi Eugenio -

Hope all is well with you at UCL. I have the run the subfields algorithm on a set of subjects using Freesurfer 6.0. All the brains were processed without much fuss. However, when I ran the following:

quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

It yielded nothing. 

Can you please help me?

Thanks,

Alan

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Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu 
                                                                                                           
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Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu 
                                                                                                           
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_______________________________________________
Freesurfer mailing list
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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.