---------- Forwarded message ----------
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Date: 2012/10/11
Subject: Re: [Freesurfer] cortical parcellation question
To: Daniel Ferreira <daniferp@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu


Hi Daniel,

no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable).

Bruce

On Thu, 11 Oct 2012, Daniel Ferreira wrote:

Thanks for the detailed information.

The mean intensity image (mean_intensity.nii) generated from frame #1 is
almost exactly what I need. This image has all the sub-cortical regions
assigned a discrete integer number (i.e. all the voxels in the left
cerebelllar grey matter = 8 and right = 47). However the whole of the
neocortex is defined as left (intensity = 3) and right (intensity = 42)
only, there are no cortical sub-divisions.

Is it possible to have the individual neocortical regions assigned a
discrete integer number; (obviously not one already assigned to the other
regions in the mean_intensity.nii image)? For example all inferior temporal
voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So
each of the regions defined in the "colortable_desikan_killiany.txt" file
found in the FREESURFER_HOME/average/ directory are also defined in the
mean_intensity.nii image?

Thanks


2012/10/6 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
      Hi Daniel

      it's in .gca format, and includes information that wouldn't fit
      in a nifti file (e.g. markov relationships). You can use
      mri_convert to extract some of the basic info though (e.g. the
      most likely class at each location and the mean intensity of the
      most likely class) using mri_convert. For example:

      mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#0
      ./labels.nii
      mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#1
      ./mean_intensity.nii


      where the #<n> syntax mean extract the nth frame from the 4D gca
      volume. Frame 0 is the most likely label and frame 1 is the mean
      intensity. Note however that there is lots more info in the .gca
      that this doesn't capture such as the MRF parameters I mentioned
      above, class variances, other class probabilities, etc....
      cheers
      Bruce




      On Thu, 4 Oct 2012, Daniel Ferreira wrote:

            Thanks Bruce,
            When you say the atlas itself is included in the
            Freesurfer distribution, do
            you mean there is a 3D version of it available in
            the download?
            Also, I am not looking for the individual subjects'
            images, I just want a
            copy of the final atlas as a 3D image in
            analyze/nifti format. (i.e. in the
            same format as the Harvard-Oxford atlas that is
            downloaded with FSL).

            Thanks a lot.

            Daniel Ferreira



            2012/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
                  Hi Daniel,

                  1. Do you mean the atlas or the parcellation
            of your subjects?
                  We cannot distribute the individual subjects
            in the atlas as the
                  data was collected under an IRB long ago that
            didn't include
                  this. The atlas itself (summary statistics
            derived from those
                  subjects) is included in the FreeSurfer
            distribution.

                  2. The subcortical areas are the same, but not
            the cortical
                  ones. That cortical parcellation is quite
            coarse, and while we
                  did implement it we were never given
            permission to distribute
                  the automated version, so it is not part of
            FreeSurfer. The
                  boundaries that we define are thus different
            than that one (and
                  since the  Harvard-Oxford one is based on
            volumetric labeling of
                  folding patterns we found that it contained a
            bunch of errors in
                  which e.g. the wrong side of a sulcus was
            labeled)

                  cheers
                  Bruce


                  On Wed, 3 Oct 2012, Daniel Ferreira wrote:

                        Dear experts,
                        I have a couple of questions regarding
            the cortical
                        parcellation atlas that
                        is used in Freesurfer:

                        1) I would like to know if it is
            possible to obtain
                        the Desikan-Killiany
                        atlas in 3D analyze/nifti format. With
            each region
                        of the brain assigned a
                        discrete integer number (for example the
            all of the
                        voxels of the left
                        inferior temporal lobe have an intensity
             = 1, or
                        the whole of the left
                        hippocampus = 2).

                        2) Are the Harvard-Oxford cortical and
            subcortical
                        atlases that can be
                        downloaded with FSL the same as the
            cortical
                        parcellation atlas that is used
                        in Freesurfer? (i.e. are the
            neuroanatomical
                        boundaries the same; does the
                        left inferior temporal cortex in the
            Freesurfer
                        cortical parcellation = the
                        left inferior temporal cortex in the
            Harvard-Oxford
                        atlas downloaded with
                        FSL)

                        Many thanks

                        Daniel Ferreira






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