creating a gca file from .mgz files - Freesurfer

23 Aug 2012

    Hopefully that doesn't scale the values I will make sure it
    doesn't. 


    When running mri_ca_train by itself after changing to float
    the next error was the Bus error.


    When running rebuild_gca_atlas.csh I was having problems with
    pbsubmit, but after avoiding that it seems to be stuck with
    mri_ca_train.


    > Date: Tue, 28 Aug 2012 17:02:51 -0400
    > From: fischl@nmr.mgh.harvard.edu
    > To: jeff_rthompson@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 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: fischl@nmr.mgh.harvard.edu
    > > > To: jeff_rthompson@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: fischl@nmr.mgh.harvard.edu
    > > > > > To: jeff_rthompson@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: fischl@nmr.mgh.harvard.edu
    > > > > > > > To: jeff_rthompson@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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