yes, you can add the various components of the cc or cingulate to get total
volume
As for the CSF label, I think it's for bits of csf that can be seen or
inferred on a T1 in sulci and maybe inferior regions. You might want to
check the original CMA (Caviness, Kenndy, et al) papers, but I imagine it's
small enough that it doesn't matter much. I believe it is *not* part of the
ventricular system
On Sun, 17 Sep 2017,
Benjamin Luerweg wrote:
hey mr greve,
hey fs community,
what do you think about adding the volumes of seperated parts of one structure
to a complete volume?
e.g. the corpus callosum or also cingulate gyrus.
is it ok to get the complete volume value by just adding the volumes of the
seperated parts?
beside that, am i right that wmparc parts of e.g. insula is just the white
matter volume?
would it be ok to add the volume of the aparc equivalent as the grey matter
volume part?
i really tried to find out what the label CSF stands for.. but beside realizing
that its not a common/regular part of the ventricle system
i couldn’t get any other informations regarding the meaning? of the CSF label.
i tried to find out whats it about by using freeview (screenshot (black part))
anyone any idea?
kind regards,
ben
Am 14.09.2017 um 20:56 schrieb Benjamin Luerweg
<luer...@students.uni-marburg.de>:
thx so far! really thank you.. do you know how to find out more about that
label?
what do you think about how to get any informations about a possible adding of
different structure parts to a „complete one“ for example the Corpus callosum
thing?
greets bl
Am 14.09.2017 um 18:40 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:
dear mr. greve,
dear fs community,
*REGARDING CSF and CSFVol:*
i still don’t understand the whole CSF and CSFVol thing.
it seems to be impossible that CSFVol ist the volume of the CSF label
because CSFVol is *bigger* than CSF.
additional to this aspect the value of the CSF label is a volume itself.
They are both index 24. the "CSF" value in aseg.stats has been partial
volume corrected, so it is a little different than "CSFVol", which is
just a count of the voxels.
so my questions again:what is the label CSF (aseg.stats) describing?
and what does it stands for? cer.spinal.fluid?
what is the label CSFVol (console) describing? and what does it stands
for if the CSF label is a volume already?
I’ve been trying to understand the meaning of the CSF (index24) by
using freeviewer.. but no chance… for me it seems to be not part of
the ventricle system as i know it? maybe you can describe it using an
image?
Not sure. This was a label supplied to us by the center for morphometric
analysis (CMA) about 20 years ago, and I can't find the docs on it. It
does not appear to be part of the ventricular system. I think it must be
some kind of of sulcal csf in the midline. I don't know why the CMA
decided to label that and not other sulcal CSF. It is pretty small and
probably will not affect your calculations that much either way
beside that: whats the advantage of this two lables beside getting the
whole ventricle volume by adding ventricles (lateral,inferior lateral,
3rd, 4th, 5th)?
I don't understand what you mean.
*REGARDING CC (corpus callosum):*
why do you think that the corpus callosum is not a 3D body? of cause
it is or what did you mean?
setting the CC parts in free viewer it seems as if it shouldn’t be a
big deal to add the separated parts of the CC to one value?!
kind regards,
benjamin luerweg
doctoral student
Am 13.09.2017 um 00:46 schrieb Douglas N Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>>:
CSFVol is actually the volume of the CSF label (index 24)
3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF
label
VentChorVol is the volume of choroird plexus, lateral ventricles, and
inferior lateral ventricles
BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ;
On 09/12/2017 02:13 PM, Benjamin Luerweg wrote:
Hey Mr. Greve,
thank your very much again!
if i understand you right, the inside the console shown up values
can’t be extracted into a separate file?
beside that, this values are of interest for me, so that i copied them
to a text file.
as you can see:Getting Brain Volume Statistics
...
SubCortGMVol 56306.000
SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343
SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352
BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231
BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034
BrainSegVolNotVent 1082437.000
CerebellumVol 145310.000
VentChorVol 23535.000
3rd4th5thCSF 3528.000
CSFVol 963.000,
OptChiasmVol 154.000
MaskVol 1526326.000
am i right that this CSFVol is the Volume of all ventricles not
including
the extra cerebral CSF?
i tried to calculate the CSFVol reverse by calculating: VentChorVol -
Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this?
and what exactly is the VentChorVol and 3rd4th5thCSF for?
im a bit confused about all this lables and im sorry for asking you so
much but i would really appreciate to solve this pity situation.
do you have a kind of an overview?
thank you in advance again,
ben luerweg
Am 11.09.2017 um 22:01 schrieb Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>>:
On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
dear fs community,
as a kind of a freesurfer greenhorn i would kindly ask you to help me
out with identifying the different labels used by freesurfer.
after using mri segstats most of the labels seem to be describing
thereselfs in proper way.
what i don’t understand are for example the different volume values
showing up inside the console after entering the segstat command.
VentChorVol what does this label explain?
Volume of all ventricles plus the volume of the chorioid plexus.
CSFVolwhy is this volume differing to the one within the segstat file?
Volume of all ventricles (not well named because it does not include
extra cerebral CSF)
and finally i would really love to know how to calculate a correct
brain to liquor ratio?!
Do you mean brain volume to total CSF volume? See above
kind regards,
ben
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