On Wed, 17 Oct 2012, Daniel Ferreira wrote:
Hello again,
Thanks for all the information Bruce.
Is it not possible to back-project the regions defined in the 2D
surface-based spherical coordinate system onto the mean_intensity.nii image?
As those regions in the 2D surface-based coordinate system would have been
initially defined on a 3D volume(s) and transformed (inflated) to the 2D
spherical surface?
Daniel
---------- 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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