Hi Seulgi
you can specify the fthresh and and slope on the command line using:
tksurfer ... -fthresh -fslope
or alternatively, both the min and max using
tksurfer ... -fminmax
where is the value at which the color saturates. Or you can set the
thresholds based on rank ordering of the val
Hi Satra and John,
I think you can use mris_make_face_parcellation for this. If you specify
?h.sphere it will make them uniform in the subject space, if you use
?h.sphere.reg it will be uniform in fsaverage space, and I think in
correspondence across subject.
cheers
Bruce
On Thu, 4 Oct 201
Hi Satra
I'm not positive I understand what you want. Have you tried
mris_divide_parcellation?
Bruce
On Wed, 3 Oct 2012, Satrajit Ghosh wrote:
hi john,
thanks. that's the idea, but what i want is that sub-division is done within
regions that are either determined automatically through the fr
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_conver
Hello,
I'm working on hippocampus segmentations obtained by Freesurfer to compare
with manual and FSL segmentations. Do I have to normalize to make these
comparisons more accurate?
If so, what volume do I have to use? I've read about eTIV but I would like
to confirm if there is any value for norm
Hi Ana,
when comparing to manual labels or other segmentation methods you do not need
to normalize. But other methods and even manual segmentations may follow a
different protocol, so it can be expected that some method gives consistently
different (e.g. smaller) values.
ICV in FreeSurfer is c
Thanks a lot Martin.
I really get confused about normalization. I've already done the
comparisons and the values between methods, as you said, are different.
Although I haven't understood why, in this case, I don't have to normalize.
My advisor told me to normalize all the brain values from the pa
Hi Ana,
if you work on a study comparing groups or age effects, that analyzes
hippocampal volume, then you would usually normalize that volume. People have
different head sizes and therefore differently sized hippocampi. To remove
headsize differences researchers often normalize voumes by ICV.
It's clear now. Thank you very much.
And you're right about manual ICV, I have only two images for each patient
with the area of the biggest plan in the brain, commissural area.
Best regards,
Ana Arruda
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hi bruce,
I'm not positive I understand what you want. Have you tried
> mris_divide_parcellation?
how do i use mris_divide_parcellation? any documentation somewhere?
the basic idea is to create some form of voronoi tesselation of a region
constrained by a parameter n_sub_regions.
subj1: aparc.
Hi Satra
isn't the code enough documentation enough?? You can use it in different
ways. Try mris_divide_parcellation -help. You can either specify an area
threshold and it will split annotations along their principle eigenaxis
until they are under that (which may mean different number for diff
hi bruce,
sorry about the documentation snafu. i kept getting an error (having tried
--help, -h, -u and all the freesurfer variants) and in the end it turned
out i was operating out of a non-existent/stale directory and that's why i
wasn't getting any help!
this is very much what i needed.
cheer
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