subject:"\[Freesurfer\] quantifyHippocampalSubfields.sh"

Re: [Freesurfer] quantifyHippocampalSubfields.sh

2016-11-22 Thread Alan Francis

Wonderful. Thank you so much.

best,

Alan

On Tue, Nov 22, 2016 at 1:42 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi again,
> The command should be:
> quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt
>
>
>
> 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 18:00, Alan Francis  wrote:
>
> 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  wheel396646 Nov 16 12:24 aparc+aseg.mgz
> -rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
> -rw-rw-r--   1 afrancis  wheel226733 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  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
> -rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
> -rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21
> aseg.presurf.hypos.mgz
> -rw-rw-r--   1 afrancis  wheel226733 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  wheel480682 Nov 16 02:46 ctrl_pts.mgz
> -rw-rw-r--   1 afrancis  wheel130178 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  wheel109443 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  wheel110421 Nov 16 12:09 rh.ribbon.mgz
> -rw-rw-r--   1 afrancis  wheel207344 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  wheel377180 Nov 16 05:56 wm.asegedit.mgz
> -rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
> -rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
> -rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
> -rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
> -rw-rw-r--   1 afrancis  wheel447425 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  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

Re: [Freesurfer] quantifyHippocampalSubfields.sh

2016-11-22 Thread Iglesias Gonzalez, Eugenio

Hi again,
The command should be:
quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt



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 18:00, Alan Francis 
> wrote:

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  wheel396646 Nov 16 12:24 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  wheel226733 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  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
-rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  wheel226733 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  wheel480682 Nov 16 02:46 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  wheel130178 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  wheel109443 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  wheel110421 Nov 16 12:09 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel207344 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  wheel377180 Nov 16 05:56 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
-rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
-rw-rw-r--   1 afrancis  wheel447425 Nov 16 12:36 wmparc.mgz

thanks so much,

Alan

On Tue, Nov 22, 2016 at 12:33 PM, Iglesias Gonzalez, Eugenio 
> 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 
> 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

--

Re: [Freesurfer] quantifyHippocampalSubfields.sh

2016-11-22 Thread Alan Francis

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  wheel396646 Nov 16 12:24 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  wheel226733 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  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
-rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  wheel226733 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  wheel480682 Nov 16 02:46 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  wheel130178 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  wheel109443 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  wheel110421 Nov 16 12:09 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel207344 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  wheel377180 Nov 16 05:56 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
-rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
-rw-rw-r--   1 afrancis  wheel447425 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  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 
> afran...@mclean.harvard.edu
>
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> ___
> Freesurfer

Re: [Freesurfer] quantifyHippocampalSubfields.sh

2016-11-22 Thread Iglesias Gonzalez, Eugenio

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 
> 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
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
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Freesurfer@nmr.mgh.harvard.edu
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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] quantifyHippocampalSubfields.sh

2016-11-22 Thread Alan Francis

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 
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] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

2015-06-11 Thread Eugenio Iglesias

Hi Carl,

the use of quantifyHippocampalSubfields.sh is:

quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory]

Simply run 
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
or
quantifyHippocampalSubfields.sh T1 test_no-T1.txt 
/Applications/freesurfer/subjects/RBrain
 and everything should work

Cheers,

/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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- Original Message -
From: Carl Anderson remfr...@gmail.com
To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, June 10, 2015 6:54:55 PM
Subject: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current  
version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz



Hi All, 


I have been using the quantifyHippocampalSubfields.sh from build 20150507 with 
no problems. 


However when I try to run the script in the new build (20150610) it fails if I 
run with the T1 flag or without. 


here is the result with T1: 



vermisii:RBrain carlanderson$ 
Gathering results from subjects in: 
test_T1.txt 
Using the suffix name: 
T1 
And writing them to: 
subfieldAnalysis_T1_v1.0 
/Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 8: cd: 
test_T1.txt: No such file or directory 
failed to do cd test_T1.txt 
vermisii:RBrain carlanderson$ 




if I omit the T1 flag: 



vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh 
subfieldAnalysis_T1_v1.0 test_no-T1.txt 
Gathering results from subjects in: 
/Applications/freesurfer/subjects/RBrain 
Using the suffix name: 
subfieldAnalysis_T1_v1.0 
And writing them to: 
test_no-T1.txt 
vermisii:RBrain carlanderson$ 


Hope this helps, 


Carl 



-- 

•~~•~~•~~•~~•~~•~~•~~• 

Carl M. Anderson, Ph.D. (mail stop 204) 
Assistant Professor of Psychiatry, 
Harvard Medical School  
The Neuroimaging Center, 
McLean Hospital 115 Mill St. Belmont, MA 02478 
Ph: 617-855-2972; Fax: 617-855-2770 
e-mail: remfr...@gmail.com ; carl_ander...@hms.harvard.edu 
•~~•~~•~~•~~•~~•~~•~~• 
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[Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

2015-06-10 Thread Carl Anderson

Hi All,

I have been using the quantifyHippocampalSubfields.sh from build 20150507
with no problems.

However when I try to run the script in the new build (20150610) it fails
if I run with the T1 flag or without.

here is the result with T1:

*vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh T1
subfieldAnalysis_T1_v1.0 test_T1.txt*
*Gathering results from subjects in: *
*   test_T1.txt *
*Using the suffix name: *
*   T1*
*And writing them to: *
*   subfieldAnalysis_T1_v1.0 *
*/Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 8: cd:
test_T1.txt: No such file or directory*
*failed to do cd test_T1.txt*
*vermisii:RBrain carlanderson$ *


if I omit the T1 flag:

*vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh
 subfieldAnalysis_T1_v1.0 test_no-T1.txt*
*Gathering results from subjects in: *
*   /Applications/freesurfer/subjects/RBrain *
*Using the suffix name: *
*   subfieldAnalysis_T1_v1.0*
*And writing them to: *
*   test_no-T1.txt *
*vermisii:RBrain carlanderson$ *

Hope this helps,

Carl


-- 
•~~•~~•~~•~~•~~•~~•~~•
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School 
The Neuroimaging Center,
McLean Hospital 115 Mill St.  Belmont, MA 02478
Ph: 617-855-2972;  Fax: 617-855-2770
e-mail: remfr...@gmail.com; carl_ander...@hms.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] quantifyHippocampalSubfields.sh

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Re: [Freesurfer] quantifyHippocampalSubfields.sh

[Freesurfer] quantifyHippocampalSubfields.sh

Re: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

[Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

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