Hi Tina,
> (e.g. to compute a general cortical thickness average for
> the inferior frontal gyrus using the pars orbitalis, pars opercularis and
> pars triangularis data).
instead of "merging" existing thickness-data you could create a new
label that constitutes your regions of interest. somethin
Creating a custom label and then using mris_anatomical_stats is probably
the route I would go as well. But out of curiosity, if I was combining
whole labels (and not splitting or subdividing any of them) I'd also
compute an "average" thickness weighted by the mid-thickness surface
area -- the two
Hi,
I have ran recon-all and got the Hippocampal volumes I desire from the
aseg.stats file. However, I have manually refined some of the volumes using the
tkmedit segmentation tool brushes and I now need to extract the revised volume
estimates.
I believe I can run 'mri_segstats' to obtain the
I have MATLABR2010b, on a Mac 10.6.4, using freesurfer 5.0
I am not able to getmatlab when I invoke freesurfer
Can someone help?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nott
weighting by surface area just let's you calculate the overall mean. Maybe
an easier way to do this is to draw the exact region you want on fsaverage
and use mri_label2label to map it to each of your subjects.
cheers
Bruce
On Thu, 23 Dec 2010, j janssen wrote:
Hi Tina,
(e.g. to compute a
Hi John,
mri_segstats is the right thing to do. It doesn't rerun the segmentation,
but if you rerun the command you find can in the scripts/recon-all.log file
it will do things like correct for partial volume effects, which is a big
deal in the hippocampus.
cheers
Bruce
On Thu, 23 Dec 2010, M
Hi,
I want to use FreeSurfer to analyze a longitudinal study. For each
subject in my study, I already used FreeSurfer 4.2 to perform the
cross-sectional analysis. However, FreeSurfer 4.2 did not have a
longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for
this purpose.
My question is:
So I hit a snag...
I can extract the ROIs that I want and combine them into a single binary
mask( allWM.mgz ). I can then run mri_mc on that mask like this.
mri_mc allWM.mgz 1 AllWhite
this generates a surface lh.AllWhite which i then move to the subjects
surf directory.
I can view the surface
Dear all,
Thank you very much for all of the comments.
I do agree with creating a custom label, but for now I only have access to
the
parcellated products. I just wanted to reduce my data's dimensionality,
because
of the limitations imposed by the brain network analysis technique.
Best,
Hi Luke
surf2surf using sphere.reg uses the surface based registration isn't what you
want. CVS should work, but I'm not sure Lilla has written anything to apply is
to a surface. You could apply it to your volume mask then tessellate that I
guess
Bruce
On Dec 23, 2010, at 10:13 AM, Luke Bloy
Hello,
I'm interested in converting my cortical thickness maps to NIFTI files. Can you
give me more information about how to do so?
Also, is it possible to analyze freesurfer cortical thickness maps in AFNI
(this is why I'm asking the question re conversion to NIFTI)? It seems as
though my mod
Rong,
You should wait until 5.1 comes out and use that to rerun your
cross-sectionals (which will have to be rerun to match a newer version)
and use that longitudinal stream which will be the most reliable.
Allison
On Thu, 23 Dec 2010, rong chen wrote:
> Hi,
> I want to use FreeSurfer to analyz
Dear all,
I would appreciate any help about this point.
I have a ROI created after a group comparison using functional data. I
would like to explore the cortical thickness of this ROI to understand if
differences in connectivity are linked to volumetric/thickness
differences.
I followed the instruc
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