Re: [Freesurfer] HSF in 5.3
Works beautifully - Thanks so much Eugenio. Have a great weekend. On Fri, Jan 29, 2016 at 10:33 AM, Eugenio Iglesias 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" > *To: *"Eugenio Iglesias" , "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 staff387540 Dec 22 23:27 aparc+aseg.mgz > -rw-rw-r-- 1 afrancis staff418008 Dec 22 23:29 aparc.a2009s+aseg.mgz > -rw-rw-r-- 1 afrancis staff223392 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 staff222988 Dec 22 17:34 aseg.auto_noCCseg.mgz > -rw-rw-r-- 1 afrancis staff328176 Dec 22 23:29 aseg.mgz > -rw-rw-r-- 1 afrancis staff223419 Dec 22 23:25 > aseg.presurf.hypos.mgz > -rw-rw-r-- 1 afrancis staff223392 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 staff482728 Dec 22 14:08 ctrl_pts.mgz > -rw-rw-r-- 1 afrancis staff129128 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 staff107428 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 staff109623 Dec 22 23:13 rh.ribbon.mgz > -rw-rw-r-- 1 afrancis staff203963 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 staff382039 Dec 22 17:42 wm.asegedit.mgz > -rw-rw-r-- 1 afrancis staff382750 Dec 22 17:42 wm.mgz > -rw-rw-r-- 1 afrancis staff415355 Dec 22 17:41 wm.seg.mgz > -rw-rw-r-- 1 afrancis staff435034 Dec 22 23:39 wmparc.mgz > > thank you, > > Alan > > > On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias > 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" >> *To: *"Eugenio Iglesias" >> *Cc: *"Freesurfer support list" >> *Sent: *Thursday, January 28, 2016 9:18:
Re: [Freesurfer] HSF in 5.3
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" To: "Eugenio Iglesias" , "Freesurfer support list" 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: BQ_BEGIN Hi Alan,
Re: [Freesurfer] 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 staff387540 Dec 22 23:27 aparc+aseg.mgz -rw-rw-r-- 1 afrancis staff418008 Dec 22 23:29 aparc.a2009s+aseg.mgz -rw-rw-r-- 1 afrancis staff223392 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 staff222988 Dec 22 17:34 aseg.auto_noCCseg.mgz -rw-rw-r-- 1 afrancis staff328176 Dec 22 23:29 aseg.mgz -rw-rw-r-- 1 afrancis staff223419 Dec 22 23:25 aseg.presurf.hypos.mgz -rw-rw-r-- 1 afrancis staff223392 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 staff482728 Dec 22 14:08 ctrl_pts.mgz -rw-rw-r-- 1 afrancis staff129128 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 staff107428 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 staff109623 Dec 22 23:13 rh.ribbon.mgz -rw-rw-r-- 1 afrancis staff203963 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 staff382039 Dec 22 17:42 wm.asegedit.mgz -rw-rw-r-- 1 afrancis staff382750 Dec 22 17:42 wm.mgz -rw-rw-r-- 1 afrancis staff415355 Dec 22 17:41 wm.seg.mgz -rw-rw-r-- 1 afrancis staff435034 Dec 22 23:39 wmparc.mgz thank you, Alan On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias 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" > *To: *"Eugenio Iglesias" > *Cc: *"Freesurfer support list" > *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 > 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 discla
Re: [Freesurfer] HSF in 5.3
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" To: "Eugenio Iglesias" Cc: "Freesurfer support list" 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 afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 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 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.
Re: [Freesurfer] 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 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" > *To: *"Freesurfer support list" , > "eiglesias" > *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 > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *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 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.
Re: [Freesurfer] HSF in 5.3
Hello All, I have run my data through free surfer 5.1. If I run recon-all distributed with free surfer 6 as follows /Applications/freesurfer6/bin/recon-all -s bert -brainstem-structures where bert was created using freesurfer 5.1, will it work ? Best Ri - Original Message - From: Eugenio Iglesias To: Alan Francis Cc: Freesurfer support list Sent: Fri, 11 Dec 2015 12:51:24 -0500 (EST) Subject: Re: [Freesurfer] HSF in 5.3 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" To: "Freesurfer support list" , "eiglesias" 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 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.
Re: [Freesurfer] HSF in 5.3
Thanks for the very quick reply Eugenio. Will download the 6.0 beta. Alan On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias 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" > *To: *"Freesurfer support list" , > "eiglesias" > *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 > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *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 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.
Re: [Freesurfer] HSF in 5.3
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" To: "Freesurfer support list" , "eiglesias" 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 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.