Works beautifully - Thanks so much Eugenio. Have a great weekend. On Fri, Jan 29, 2016 at 10:33 AM, Eugenio Iglesias <e.igles...@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" <alandarkene...@gmail.com> > *To: *"Eugenio Iglesias" <e.igles...@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.igles...@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" <alandarkene...@gmail.com> >> *To: *"Eugenio Iglesias" <e.igles...@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.igles...@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" <alandarkene...@gmail.com> >>> *To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, >>> "eiglesias" <eigles...@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 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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