Works beautifully - Thanks so much Eugenio. Have a great weekend.

On Fri, Jan 29, 2016 at 10:33 AM, Eugenio Iglesias <e.iglesias@bcbl.eu> wrote:
Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID of the analysis:

quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt

Let me know if it doesn't work!

Cheers,

/Eugenio



Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Alan Francis" <alandarkenergy@gmail.com>
To: "Eugenio Iglesias" <e.iglesias@bcbl.eu>, "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, January 29, 2016 4:17:06 PM

Subject: Re: HSF in 5.3

Hi Eugenio:

Here is the list of files in the 'mri' directory of a given subject:

afrancis-mac:HSF afrancis$ cd Smoke_d004/
afrancis-mac:Smoke_d004 afrancis$ cd mri
afrancis-mac:mri afrancis$ ls -la
total 93464
drwxrwxr-x  47 afrancis  staff      1598 Dec 23 01:05 .
drwxr-xr-x  13 afrancis  staff       442 Dec 22 13:14 ..
-rw-r--r--@  1 afrancis  staff      6148 Dec 18 15:11 .DS_Store
-rwxrw-rw-   1 afrancis  staff         0 Dec  8 16:52 .xdebug_mris_calc
-rw-rw-r--   1 afrancis  staff   5497095 Dec 22 13:25 T1.mgz
-rw-rw-r--   1 afrancis  staff    387540 Dec 22 23:27 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  staff    418008 Dec 22 23:29 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  staff    223392 Dec 22 17:35 aseg.auto.mgz
-rw-rw-r--   1 afrancis  staff      1545 Dec 22 17:06 aseg.auto_noCCseg.label_intensities.txt
-rw-rw-r--   1 afrancis  staff    222988 Dec 22 17:34 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  staff    328176 Dec 22 23:29 aseg.mgz
-rw-rw-r--   1 afrancis  staff    223419 Dec 22 23:25 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  staff    223392 Dec 22 17:35 aseg.presurf.mgz
-rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.finalsurfs.mgz
-rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.mgz
-rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.auto.mgz
-rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.mgz
-rw-rw-r--   1 afrancis  staff    482728 Dec 22 14:08 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  staff    129128 Dec 22 17:43 filled.mgz
-rw-rw-r--   1 afrancis  staff     69210 Dec 23 00:36 lh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  staff     66085 Dec 23 00:36 lh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  staff       286 Dec 23 00:36 lh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  staff    107428 Dec 22 23:13 lh.ribbon.mgz
-rw-rw-r--   1 afrancis  staff     20564 Dec 22 13:51 mri_nu_correct.mni.log
-rw-rw-r--   1 afrancis  staff     17647 Dec 22 13:22 mri_nu_correct.mni.log.bak
-rw-rw-r--   1 afrancis  staff   1314015 Dec 22 14:08 norm.mgz
-rw-rw-r--   1 afrancis  staff   3901730 Dec 22 13:51 nu.mgz
-rw-rw-r--   1 afrancis  staff   2735369 Dec 22 16:29 nu_noneck.mgz
drwxrwxr-x   3 afrancis  staff       102 Dec  8 15:38 orig
-rw-rw-r--   1 afrancis  staff   6690110 Dec 22 13:14 orig.mgz
-rw-rw-r--   1 afrancis  staff   6922353 Dec 22 13:22 orig_nu.mgz
-rwxrw-r--   1 afrancis  staff  10717567 Dec 22 13:14 rawavg.mgz
-rw-rw-r--   1 afrancis  staff     69132 Dec 23 01:05 rh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  staff     62976 Dec 23 01:05 rh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  staff       286 Dec 23 01:05 rh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  staff    109623 Dec 22 23:13 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  staff    203963 Dec 22 23:13 ribbon.mgz
-rw-rw-r--   1 afrancis  staff       119 Dec 22 17:40 segment.dat
-rw-rw-r--   1 afrancis  staff      1545 Dec 22 15:02 talairach.label_intensities.txt
-rw-rw-r--   1 afrancis  staff       214 Dec 22 14:05 talairach.log
-rw-rw-r--   1 afrancis  staff       214 Dec 22 13:42 talairach_with_skull.log
-rw-rw-r--   1 afrancis  staff       214 Dec 22 16:51 talairach_with_skull_2.log
drwxrwxr-x  13 afrancis  staff       442 Dec 22 17:35 transforms
-rw-rw-r--   1 afrancis  staff    382039 Dec 22 17:42 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  staff    382750 Dec 22 17:42 wm.mgz
-rw-rw-r--   1 afrancis  staff    415355 Dec 22 17:41 wm.seg.mgz
-rw-rw-r--   1 afrancis  staff    435034 Dec 22 23:39 wmparc.mgz

thank you,

Alan


On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias <e.iglesias@bcbl.eu> wrote:
Hi Alan,
can you please list the files in the mri directory of any of the subjects and send me the output?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Alan Francis" <alandarkenergy@gmail.com>
To: "Eugenio Iglesias" <e.iglesias@bcbl.eu>
Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, January 28, 2016 9:18:46 PM
Subject: Re: HSF in 5.3

Hi Eugenio:

As you advised, I ran the following command:

afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 Nicotine_HSF.txt
Gathering results from subjects in:
   /Users/afrancis/Desktop/Connectome/HSF/
Using the suffix name:
   Smoke_e024
And writing them to:
   Nicotine_HSF.txt

However, when I opened the Nicotine_HSF.txt, there was nothing there. The Subjects directory is the same folder.

Please advice - thanks so much,

Alan

On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias <e.iglesias@bcbl.eu> wrote:
Hi Alan,
the subfield module is not present in 5.3; you'll need to download the development version (or wait until 6.0 is released, which should be pretty soon=.
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Alan Francis" <alandarkenergy@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, "eiglesias" <eiglesias@bcbl.eu>
Sent: Friday, December 11, 2015 6:36:42 PM
Subject: HSF in 5.3

Hi Eugenio:
I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message.

[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields

ERROR: Flag -hippocampal-subfields unrecognized.

-s Smoke_d004 -hippocampal-subfields

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015


For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


I tried adding the  -hippocampal-subfields-T1 but that did not work too.


thanks,


Alan





--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|