No, the last 3 columns (Min Max Range) are the minimum, maximum, and range (maximum - minimum) or the values in path.pd.nii.gz.
But it does look like mri_segstats can get you what you want, if you use a binarized version of path.pd.nii.gz. Use mri_binarize (possibly with a threshold, if you want to threshold the distribution) on path.pd.nii.gz, which will give you an output volume that has 1 inside and 0 outside the pathway. Then you run mri_segstats on that binarized volume. What you want (the volume of the pathway inside each structure) will be the sum of the 1's of the pathway inside each structure. Because mri_segstats doesn't give you the sum but it does give you the mean, you'll have to calculate the sum as the mean multiplied by the total number of voxels in the same structure. So column "Mean" multiplied by column "NVoxels" will give you the number of voxels in each structure that intersect the pathway.
On Thu, 24 Oct 2013, Lucia Billeci wrote:
Dear Anastasia,
yes I was referring to the last three columns. So for the last three columns
is it right what I told you? Is it the volume of the path?
Lucia
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
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Il giorno 23/ott/2013, alle ore 19:24, Anastasia Yendiki ha scritto:
Hi Lucia - The columns "NVoxels Volume_mm3" in the mri_segstats
output are the volumes of each of the structures in the
aparc+aseg, so those columns have nothing to do with the path.
The last few columns, "Mean StdDev Min Max Range", are related
to the values in path.pd.nii.gz.
Hope this helps,
a.y
On Wed, 23 Oct 2013, Lucia Billeci wrote:
Dear Anastasia,
I tried the command you suggested me and i obtained
the output I attach to the mail.
I would like to ask you if I understood well shot it
means. In this case left uncinatus connects the
following cortex areas:
ctx-lh-fusiform
ctx-lh-inferiortemporal
ctx-lh-lateralorbitofrontal
ctx-lh-medialorbitofrontal
ctx-lh-middletemporal
ctx-lh-rostralanteriorcingulate
ctx-lh-superiortemporal
ctx-lh-temporalpole
ctx-lh-insula
and for each area I have the volume of the path. Is
it correct?
Thanks
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
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Il giorno 18/ott/2013, alle ore 17:32, Anastasia
Yendiki ha scritto:
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
_ _ _ _
_ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
_
The
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you believe this e-mail was
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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
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contains patient
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dispose of the
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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
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 Freesurfer@nmr.mgh.harvard.edu 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 dispose of the e-mail.
