Hi Lucia - You can probably do that with mri_segstats. Try something like:
mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i
dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz
And similarly for any other pathway. See the mri_segstats help for more
usage info. Let me know if this gives you what you need.
a.y
On Fri, 18 Oct 2013, Lucia Billeci wrote:
Thanks Anastasia, this is useful for visualization. But to construct a table
with for each tracts the parcellation regions that it connects do I need to
look at the image?
Lucia
On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote:
Hi Lucia - You can look at the tracula output over the cortical
parcellation and subcortical segmentation in the individual's
diffusion space like this:
freeview dmri/dtifit_FA.nii.gz
dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv
dpath/merged_avg33_mni_bbr.mgz
Hope this helps,
a.y
On Fri, 18 Oct 2013, Lucia Billeci wrote:
Dear Anastasia and all,
how can I understand which are the region of the
brain in which the brain
base been parecellated that each tract generated by
TRACULA connect?
For example if I look at the left uncinate
fascicles how can I know which
are the ROIs of the statistical output from the
cortical parcellation that
it connects?
Thanks
Lucia
On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote:
Hi Anastasia,
thanks for you answer. Now I have understood the
meaning of that
parameter.
Best regards
Lucia
On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki
wrote:
Hi Lucia - It's how many sample paths were
drawn to
produce the probability distribution of the
path
(path.pd.nii.gz). It depends on the
configuration
parameters (nsample, nkeep), so it'll be the
same if these
configuration parameters are the same.
Hope this helps,
a.y
On Mon, 14 Oct 2013, Lucia Billeci wrote:
Dear all,
I noticed that in the TRACULA statistics
output files (pathstats.overall.txt) the
variable "Count" that
should indicate the number of sample
paths in
the WM tract is the same for all the
computed
tract. Could
anyone tell me why this happen?
Thanks a lot
Regards
Lucia
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_
Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC)
National Research Council (CNR)
via Moruzzi 1, 56124, Pisa
ITALY
Tel: +39-0506213204
e-mail: lucia.bill...@ifc.cnr.it
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Dr. Lucia Billeci, PhD, Engineer
National Research Council of Italy (CNR)
Institute of Clinical Physiology (IFC)
via Moruzzi, 1 Pisa - Italy
http://www.ifc.cnr.it
Tel. +39-050-3152182 Cell. +39-339-1863902
Email: lucia.bill...@ifc.cnr.it
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HelpLine at
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but does not contain patient information, please
contact the sender
and properly
dispose of the e-mail.
Dr. Lucia Billeci, PhD, Engineer
National Research Council of Italy (CNR)
Institute of Clinical Physiology (IFC)
via Moruzzi, 1 Pisa - Italy
http://www.ifc.cnr.it
Tel. +39-050-3152182 Cell. +39-339-1863902
Email: lucia.bill...@ifc.cnr.it
Dr. Lucia Billeci, PhD, Engineer
National Research Council of Italy (CNR)
Institute of Clinical Physiology (IFC)
via Moruzzi, 1 Pisa - Italy
http://www.ifc.cnr.it
Tel. +39-050-3152182 Cell. +39-339-1863902
Email: lucia.bill...@ifc.cnr.it
_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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