HSF in 5.3

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Alan Francis

11 Dec 2015 11 Dec '15

12:36 p.m.

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 ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Eugenio Iglesias

11 Dec 11 Dec

12:51 p.m.

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 Francis

12:53 p.m.

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 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 ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Ritobrato Datta

3:30 p.m.

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

----- Original Message ----- From: Eugenio Iglesias e.iglesias@bcbl.eu To: Alan Francis alandarkenergy@gmail.com Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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

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 Francis

28 Jan 28 Jan

3:18 p.m.

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 ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Eugenio Iglesias

5:14 p.m.

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:

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 afrancis@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 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan Francis

29 Jan 29 Jan

10:17 a.m.

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

Eugenio Iglesias

10:33 a.m.

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:

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:

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:

BQ_BEGIN

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

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

BQ_END

Alan Francis

4:06 p.m.

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

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Alan Francis
Eugenio Iglesias
Ritobrato Datta