Re: [Freesurfer] HSF in 5.3

2016-01-29 Thread Alan Francis 
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

Re: [Freesurfer] HSF in 5.3

2016-01-29 Thread Eugenio Iglesias 
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

Re: [Freesurfer] HSF in 5.3

2016-01-29 Thread Alan Francis 
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"

Re: [Freesurfer] HSF in 5.3

2016-01-28 Thread Eugenio Iglesias 
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

2016-01-28 Thread Alan Francis 
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

2015-12-11 Thread Eugenio Iglesias 
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

2015-12-11 Thread Alan Francis 
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

2015-12-11 Thread Ritobrato Datta 
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 <e.igles...@bcbl.eu>
To: Alan Francis <alandarkene...@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 


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 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 
___
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.