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 <fis...@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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