does that scale the values? Hopefully not. It sounds like things don't fail
after you changed to float until you get the pbsubmit problem, correct?
On Tue, 28 Aug 2012, Jeff Thompson wrote:
To change to type Float I used:
fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
Alloybrain_mask_LUTComplete_float.nii.gz -odt float
I will try some other methods for changing the data type, but if that isn't
the issue are there other cases of getting similar errors from mri_ca_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? Make sure it doesn't scale the
> inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our
> compute cluster queueing system which is what the pbsubmit script is.
> You'll need to modify it to use whatever cluster you are using or to run
> them in series
>
> cheers
> Bruce
> On Tue, 28 Aug 2012, Jeff Thompson wrote:
>
> >
> > Hello,
> > When running the mri_ca_train I am getting a Bus error near the
beginning of
> > it.
> >
> > 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz
-T1
> > norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's
> > mri/Alloybrain_mask_LUTComplete_float.mgz directory
> > reading T1 data from subject's mri/norm.mgz directory
> > training on 1 subject and writing results to single_oneAlloy.gca
> > gcaAllocMax: node dims 64 64 64
> > gcaAllocMax: prior dims 128 128 128
> > gcaAllocMax: max_labels 4
> >***************************************************************************
> > processing subject Alloy, 1 of 1...
> > reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz
> > Bus error
> > '
> > Previously it was giving an error saying that :"mri_ca_train:
segmentation
> > file
> >
Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is
> > not type UCHAR or FLOAT"
> >
> > So I changed the file type to float to get rid of that.
> > Any ideas?
> >
> > When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found
> > error. If I have a cluster to use, but am able to just load everything
onto
> > it 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 a gca file from .mgz files
> > >
> > > Hi Jefff
> > > you can give mri_ca_normalize a flag to tell it to use a manual
> > > segmentation instead of the gca. Try -seg <manual seg volume>. Then
the
> > > gca name won't matter - it should ignore it.
> > >
> > > You could use label2label I guess, although if it's accurate across
brains
> > > then you probably don't need it and can just build the gca from a
handful
> > > of brains instead of the dozens we need for humans
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Mon, 27 Aug 2012, Jeff
> > > Thompson wrote:
> > >
> > > > Hello,
> > > > Okay, but from looking at the recon-all pipeline it looks like to
> > generate
> > > > the norm.mgz file the .gca atlas is needed first. If I create the
> > > > seg_edited.mgz file from my manually labelled file can I use that in
> > > > rebuild_gca_atlas.csh to generate the .gca atlas? This would
incorporate
> > the
> > > > mri_ca_train, is that correct?
> > > >
> > > > The other question I have is regarding mri_label2label. If I have
> > manually
> > > > labelled one brain from my set, can I use mri_label2label to convert
> > these
> > > > labels to other dog brains in my set if they have been registered to
the
> > > > first brain used?
> > > >
> > > > Thank you,
> > > >
> > > >
> > > >
> > > > Jeff 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. 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_ca_train
> > > > >
> > > > > cheers
> > > > > Bruce
> > > > >
> > > > >
> > > > > On Thu, 23
> > > > > Aug 2012, Jeff Thompson wrote:
> > > > >
> > > > > > >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.mgz
> > > > > >
> > > > > > where:
> > > > > >
> > > > > > *
> > > > > >
> > > > > > means --> the mean intensity of the most likely label
> > > > > >
> > > > > > *
> > > > > >
> > > > > > labels --> indices of the most likely label at each voxel
(indices
> > refer
> > > > > > to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)
> > > > > >
> > > > > > *
> > > > > >
> > > > > > priors --> the probability that that label occurs at that voxel
> > > > > >
> > > > > >
> > > > > > Is it possible to go the other way? I want to create the
labels.mgz
> > file
> > > > and
> > > > > > the others manually, and turn that into the .gca file with
> > mri_convert.
> > > > > >
> > > > > > Can this be done?
> > > > > >
> > > > > > Thank you,
> > > > > >
> > > > > > Jeff Thompson
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
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