Hi Pradeep
pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you
don't have a cluster you should just run the commands that it runs.
cheers
Bruce
On Mon, 19 Jan 2015, pradeep mahato wrote:
> Hello experts,
> I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I
Hello experts,
I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to
create a atlas using previous registered subjects.
It does not complete the mri_ca_normalize phase and stops there. It shows
pbsubmit: Command not found as error.
Please correct me. Also attaching the rebuil
d the mri_convert
>>> conform with the rt nearest , but the label values seemed to still be off.
>>> The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
>>> Any recommendations to solve this problem?
>>> Thank you,
>>> Jeff Thompson
&g
alues are way off. I tried the mri_convert
>> conform with the rt nearest , but the label values seemed to still be off.
>> The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
>> Any recommendations to solve this problem?
>> Thank you,
>>
conform with the rt nearest , but the label values seemed to still be off.
The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
Any recommendations to solve this problem?
Thank you,
Jeff Thompson
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> Fr
ried the mri_convert
>
> conform with the rt nearest , but the label values seemed to still be off.
>
> The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
>
> Any recommendations to solve this problem?
>
> Thank you,
>
> Jeff Thompson
>
>
I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
Any recommendations to solve this problem?
Thank you,
Jeff Thompson
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> From: ni...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: fis...@nmr.mgh
>
>
>
>
>
> ______________
> CC: freesurfer@nmr.mgh.harvard.edu
> From: fis...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> Date: Tue, 28 Aug 2012 20:12:45 -0400
> To: jeff_rtho
arvard.edu
From: fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating a gca file from .mgz files
Date: Tue, 28 Aug 2012 20:12:45 -0400
To: jeff_rthomp...@hotmail.com
Oh, so you still got a bus error? I didn't realize that. Make sure the seg
volumes are ok
On Aug 28, 2012, at 6:10
mr.mgh.harvard.edu
> > To: jeff_rthomp...@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: RE: [Freesurfer] creating a gca file from .mgz files
> >
> > does that scale the values? Hopefully not. It sounds like things don't fail
> > after
stuck with mri_ca_train.
> Date: Tue, 28 Aug 2012 17:02:51 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] creating a gca file from .mgz files
>
> does that scale the values? Hopefully not. I
harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] creating a gca file from .mgz files
>
> how did you change the type to float? Make sure it doesn't scale the
> inputs if that is the segmentation volume. rebuild_gca_atlas.
train?
thanks,
Jeff
> Date: Tue, 28 Aug 2012 16:37:19 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] creating a gca file from .mgz files
>
> how did you change the type to float?
t and then run it, can I comment out all of the pbsubmit lines?
Thank you for all the help,
Jeff
> Date: Mon, 27 Aug 2012 12:00:13 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] creating
for all the help,
Jeff
> Date: Mon, 27 Aug 2012 12:00:13 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] creating a gca file from .mgz files
>
> Hi Jefff
> you can give mri_ca_norma
h.harvard.edu
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
>
> Hi Jeff
>
> it's more complicated than that. You need a .mgz volume for every subject
> you want to train on that contains the labels, and an accompanying
> intensity volume (we usually
Thompson
> Date: Sat, 25 Aug 2012 11:11:46 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
>
> Hi Jeff
>
> it's more complicated than that.
Hi Jeff
it's more complicated than that. You need a .mgz volume for every subject
you want to train on that contains the labels, and an accompanying
intensity volume (we usually use the norm.mgz for this purpose). Then we
extract statistics to create the .gca across these subjects using
mri_c
>From the gcaFormat freesurfer wiki page I know that: The .gca file is composed
>of three volumes, which can be extracted like this:mri_convert atlas.gca -nth
>0 means.mgz
mri_convert atlas.gca -nth 1 labels.mgz
mri_convert atlas.gca -nth 2 priors.mgzwhere:means --> the mean intensity of
the mo
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