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
> >
> >
> >
> >
>
>
> 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.