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.igles...@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 <alandarkene...@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 > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > * Alan N. Francis PhD* > Instructor - Imaging Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > _______________________________________________ > Freesurfer mailing list > 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.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. > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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