Re: [Freesurfer] labels used by freesurfer

2017-09-18 Thread Douglas N Greve 
Yes, same for cingulate. I don't really know what you are referring to 
in terms of mixed structures. Maybe some subcortical structures are 
thought of in this way


On 09/18/2017 05:52 PM, Benjamin Luerweg wrote:
> is that the same for the cingulate gyrus? or is cyng really a white and grey 
> matter splitted structure?
>
>
>> Am 18.09.2017 um 23:50 schrieb Douglas N Greve :
>>
>>
>>
>> On 09/18/2017 05:47 PM, Benjamin Luerweg wrote:
>>> *am i right that numbers out of the wmparc file of e.g. the insula
>>> are just the volumes of the white matter part of e.g. the insula?
>>> *
>> *no, insula is a gray matter cortical structure. the insulaWM in the
>> wmparc file is just WM that is closer to insula than to any other
>> cortical structure. probably it is related to insula, but it should not
>> be considered part of insula*
>>> *would it be ok to add the volumes of the aparc file as the grey
>>> matter volume.. to get the complete*
>>> *volume of e.g. the insula? *
>>>
>>> kind regards
>>>
>>>
>>>
>>>
 Am 18.09.2017 um 17:49 schrieb Benjamin Luerweg
 >:

 hey all!

 ok.. sorry guys i detected a calculation mistake… !!

 and the now calculated values seem to be close enough to be correct…

 anyway… the brainsegvol - brainsegvolnotvent number is different to
 adding all ventricle volumes number like —> 21782 and 20980 …
 any idea why ?

 which way of calculating the whole ventricle volume value is more
 precise? adding the different ventricle parts or subtracting
 brainsegvolnotvent from brainsegvol?



 last question:
 *
 *
 *am i right that numbers out of the wmparc file of e.g. the
 insula are just the volumes of the white matter part of e.g. the
 insula?
 *
 *would it be ok to add the volumes of the aparc file as the grey
 matter volume.. to get the complete*
 *volume of e.g. the insula? *

 kind regards
 b.l.



> Am 18.09.2017 um 00:08 schrieb Douglas Greve
> >:
>
> Can you post the numbers for each item? Your first calculation is
> over 200 thousand mm3 (10x the 2nd calc) which suggests a math error
>
>
> On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
>> alright.. so far…BUT:
>>
>> Ive tried to get the volume of the ventricle system by using two
>> different calculations.
>>
>> first of all i tried to get the volume by: brainsegvol -
>> brainsegvolnotvent
>> than i tried to simply add all the seprate parts of the ventricle
>> system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th
>> ventricle)
>>
>> after doing this i realized that the two values were differing like
>> -> 217820,00 (first calculation) and 20115,8998 (second
>> calculation)
>> any ideas why the difference is that big?
>>
>>
>> kind regards
>>
>>
>>
>>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl
>>> >:
>>>
>>> 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
>

Re: [Freesurfer] labels used by freesurfer

2017-09-18 Thread Benjamin Luerweg 
is that the same for the cingulate gyrus? or is cyng really a white and grey 
matter splitted structure?


> Am 18.09.2017 um 23:50 schrieb Douglas N Greve :
> 
> 
> 
> On 09/18/2017 05:47 PM, Benjamin Luerweg wrote:
>> 
>> *am i right that numbers out of the wmparc file of e.g. the insula 
>> are just the volumes of the white matter part of e.g. the insula?
>> *
> *no, insula is a gray matter cortical structure. the insulaWM in the 
> wmparc file is just WM that is closer to insula than to any other 
> cortical structure. probably it is related to insula, but it should not 
> be considered part of insula*
>> 
>> *would it be ok to add the volumes of the aparc file as the grey 
>> matter volume.. to get the complete*
>> *volume of e.g. the insula? *
>> 
>> 
>> kind regards
>> 
>> 
>> 
>> 
>>> Am 18.09.2017 um 17:49 schrieb Benjamin Luerweg 
>>> >> >:
>>> 
>>> hey all!
>>> 
>>> ok.. sorry guys i detected a calculation mistake… !!
>>> 
>>> and the now calculated values seem to be close enough to be correct…
>>> 
>>> anyway… the brainsegvol - brainsegvolnotvent number is different to 
>>> adding all ventricle volumes number like —> 21782 and 20980 …
>>> any idea why ?
>>> 
>>> which way of calculating the whole ventricle volume value is more 
>>> precise? adding the different ventricle parts or subtracting 
>>> brainsegvolnotvent from brainsegvol?
>>> 
>>> 
>>> 
>>> last question:
>>> *
>>> *
>>> *am i right that numbers out of the wmparc file of e.g. the 
>>> insula are just the volumes of the white matter part of e.g. the 
>>> insula?
>>> *
>>> 
>>> *would it be ok to add the volumes of the aparc file as the grey 
>>> matter volume.. to get the complete*
>>> *volume of e.g. the insula? *
>>> 
>>> 
>>> kind regards
>>> b.l.
>>> 
>>> 
>>> 
 Am 18.09.2017 um 00:08 schrieb Douglas Greve 
 >:
 
 Can you post the numbers for each item? Your first calculation is 
 over 200 thousand mm3 (10x the 2nd calc) which suggests a math error
 
 
 On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
> alright.. so far…BUT:
> 
> Ive tried to get the volume of the ventricle system by using two 
> different calculations.
> 
> first of all i tried to get the volume by: brainsegvol - 
> brainsegvolnotvent
> than i tried to simply add all the seprate parts of the ventricle 
> system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th 
> ventricle)
> 
> after doing this i realized that the two values were differing like 
> -> 217820,00 (first calculation) and 20115,8998 (second 
> calculation)
> any ideas why the difference is that big?
> 
> 
> kind regards
> 
> 
> 
>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl 
>> >:
>> 
>> 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 
 >:
 
 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

Re: [Freesurfer] labels used by freesurfer

2017-09-18 Thread Douglas N Greve 


On 09/18/2017 05:47 PM, Benjamin Luerweg wrote:
>
> *am i right that numbers out of the wmparc file of e.g. the insula 
> are just the volumes of the white matter part of e.g. the insula?
> *
*no, insula is a gray matter cortical structure. the insulaWM in the 
wmparc file is just WM that is closer to insula than to any other 
cortical structure. probably it is related to insula, but it should not 
be considered part of insula*
>
> *would it be ok to add the volumes of the aparc file as the grey 
> matter volume.. to get the complete*
> *volume of e.g. the insula? *
>
>
> kind regards
>
>
>
>
>> Am 18.09.2017 um 17:49 schrieb Benjamin Luerweg 
>> > >:
>>
>> hey all!
>>
>> ok.. sorry guys i detected a calculation mistake… !!
>>
>> and the now calculated values seem to be close enough to be correct…
>>
>> anyway… the brainsegvol - brainsegvolnotvent number is different to 
>> adding all ventricle volumes number like —> 21782 and 20980 …
>> any idea why ?
>>
>> which way of calculating the whole ventricle volume value is more 
>> precise? adding the different ventricle parts or subtracting 
>> brainsegvolnotvent from brainsegvol?
>>
>>
>>
>> last question:
>> *
>> *
>> *am i right that numbers out of the wmparc file of e.g. the 
>> insula are just the volumes of the white matter part of e.g. the 
>> insula?
>> *
>>
>> *would it be ok to add the volumes of the aparc file as the grey 
>> matter volume.. to get the complete*
>> *volume of e.g. the insula? *
>>
>>
>> kind regards
>> b.l.
>>
>>
>>
>>> Am 18.09.2017 um 00:08 schrieb Douglas Greve 
>>> >:
>>>
>>> Can you post the numbers for each item? Your first calculation is 
>>> over 200 thousand mm3 (10x the 2nd calc) which suggests a math error
>>>
>>>
>>> On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
 alright.. so far…BUT:

 Ive tried to get the volume of the ventricle system by using two 
 different calculations.

 first of all i tried to get the volume by: brainsegvol - 
 brainsegvolnotvent
 than i tried to simply add all the seprate parts of the ventricle 
 system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th 
 ventricle)

 after doing this i realized that the two values were differing like 
 -> 217820,00 (first calculation) and 20115,8998 (second 
 calculation)
 any ideas why the difference is that big?


 kind regards



> Am 17.09.2017 um 20:51 schrieb Bruce Fischl 
> >:
>
> 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 
>>> >> >:
>>>
>>> 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 
 >:



 On 09/13/2017

Re: [Freesurfer] labels used by freesurfer

2017-09-18 Thread Benjamin Luerweg 

 am i right that numbers out of the wmparc file of e.g. the insula are just 
 the volumes of the white matter part of e.g. the insula?

 would it be ok to add the volumes of the aparc file as the grey matter 
 volume.. to get the complete
 volume of e.g. the insula? 


kind regards




> Am 18.09.2017 um 17:49 schrieb Benjamin Luerweg 
> :
> 
> hey all!
> 
> ok.. sorry guys i detected a calculation mistake… !! 
> 
> and the now calculated values seem to be close enough to be correct…
> 
> anyway… the brainsegvol - brainsegvolnotvent number is different to adding 
> all ventricle volumes number like —> 21782 and 20980 …
> any idea why ?
> 
> which way of calculating the whole ventricle volume value is more precise? 
> adding the different ventricle parts or subtracting brainsegvolnotvent from 
> brainsegvol?
> 
> 
> 
> last question:
> 
> am i right that numbers out of the wmparc file of e.g. the insula are 
> just the volumes of the white matter part of e.g. the insula?
> 
> would it be ok to add the volumes of the aparc file as the grey matter 
> volume.. to get the complete
> volume of e.g. the insula? 
> 
> 
> 
> kind regards
> b.l.
> 
> 
> 
>> Am 18.09.2017 um 00:08 schrieb Douglas Greve > >:
>> 
>> Can you post the numbers for each item? Your first calculation is over 200 
>> thousand mm3 (10x the 2nd calc) which suggests a math error
>> 
>> On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
>>> alright.. so far…BUT:
>>> 
>>> Ive tried to get the volume of the ventricle system by using two different 
>>> calculations.
>>> 
>>> first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent
>>> than i tried to simply add all the seprate parts of the ventricle system 
>>> (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)
>>> 
>>> after doing this i realized that the two values were differing like -> 
>>> 217820,00 (first calculation) and 20115,8998 (second calculation)
>>> any ideas why the difference is that big?
>>> 
>>> 
>>> kind regards
>>> 
>>> 
>>> 
 Am 17.09.2017 um 20:51 schrieb Bruce Fischl >:
 
 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 
>> > >:
>> 
>> 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 
>>> >> >> >>:
>>> 
>>> 
>>> 
>>> 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.

Re: [Freesurfer] labels used by freesurfer

2017-09-18 Thread Benjamin Luerweg 
hey all!

ok.. sorry guys i detected a calculation mistake… !! 

and the now calculated values seem to be close enough to be correct…

anyway… the brainsegvol - brainsegvolnotvent number is different to adding all 
ventricle volumes number like —> 21782 and 20980 …
any idea why ?

which way of calculating the whole ventricle volume value is more precise? 
adding the different ventricle parts or subtracting brainsegvolnotvent from 
brainsegvol?



last question:

 am i right that numbers out of the wmparc file of e.g. the insula are just 
 the volumes of the white matter part of e.g. the insula?

 would it be ok to add the volumes of the aparc file as the grey matter 
 volume.. to get the complete
 volume of e.g. the insula? 



kind regards
b.l.



> Am 18.09.2017 um 00:08 schrieb Douglas Greve :
> 
> Can you post the numbers for each item? Your first calculation is over 200 
> thousand mm3 (10x the 2nd calc) which suggests a math error
> 
> On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
>> alright.. so far…BUT:
>> 
>> Ive tried to get the volume of the ventricle system by using two different 
>> calculations.
>> 
>> first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent
>> than i tried to simply add all the seprate parts of the ventricle system (rh 
>> lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)
>> 
>> after doing this i realized that the two values were differing like -> 
>> 217820,00 (first calculation) and 20115,8998 (second calculation)
>> any ideas why the difference is that big?
>> 
>> 
>> kind regards
>> 
>> 
>> 
>>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl >> >:
>>> 
>>> 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 
>  >:
> 
> 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 
>> > > >>:
>> 
>> 
>> 
>> 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

Re: [Freesurfer] labels used by freesurfer

2017-09-17 Thread Douglas Greve 
Can you post the numbers for each item? Your first calculation is over 
200 thousand mm3 (10x the 2nd calc) which suggests a math error



On 9/17/17 2:55 PM, Benjamin Luerweg wrote:

alright.. so far…BUT:

Ive tried to get the volume of the ventricle system by using two 
different calculations.


first of all i tried to get the volume by: brainsegvol - 
brainsegvolnotvent
than i tried to simply add all the seprate parts of the ventricle 
system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)


after doing this i realized that the two values were differing like -> 
217820,00 (first calculation) and 20115,8998 (second calculation)

any ideas why the difference is that big?


kind regards



Am 17.09.2017 um 20:51 schrieb Bruce Fischl 
>:


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 
>:


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 
>:




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
>>:


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

Re: [Freesurfer] labels used by freesurfer

2017-09-17 Thread Benjamin Luerweg 
alright.. so far…BUT:

Ive tried to get the volume of the ventricle system by using two different 
calculations.

first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent
than i tried to simply add all the seprate parts of the ventricle system (rh 
lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)

after doing this i realized that the two values were differing like -> 
217820,00 (first calculation) and 20115,8998 (second calculation)
any ideas why the difference is that big?


kind regards



> Am 17.09.2017 um 20:51 schrieb Bruce Fischl :
> 
> 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 
>>> :
>>> 
>>> 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 >>:
 
 
 
 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
>> >

Re: [Freesurfer] labels used by freesurfer

2017-09-17 Thread Bruce Fischl 
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 
:

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 >:



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
>>:

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

Re: [Freesurfer] labels used by freesurfer

2017-09-17 Thread Benjamin Luerweg 
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 
> :
> 
> 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 > >:
>> 
>> 
>> 
>> 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 
 >>:
 
 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

Re: [Freesurfer] labels used by freesurfer

2017-09-14 Thread Benjamin Luerweg 
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 :
> 
> 
> 
> 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 
>>> >> >> >>:
>>> 
>>> 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
>  
>  > >>:
> 
> 
> 
> 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
>>

Re: [Freesurfer] labels used by freesurfer

2017-09-14 Thread Douglas N Greve 


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 
>> >:
>>
>> 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
 >:



 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

Re: [Freesurfer] labels used by freesurfer

2017-09-13 Thread Benjamin Luerweg 
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.

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?

beside that: whats the advantage of this two lables beside getting the whole 
ventricle volume by adding ventricles (lateral,inferior lateral, 3rd, 4th, 5th)?



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 :
> 
> 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 
>>>  
>>> >>:
>>> 
>>> 
>>> 
>>> 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
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu  
 >
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 
>>> 
>>> -- 
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu  
>>> >
>>> Phone Number: 617-724-2358

Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Douglas N Greve 
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 
>> >:
>>
>>
>>
>> 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
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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.
>>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Benjamin Luerweg 
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 :
> 
> 
> 
> 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
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> 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.
> 

___
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.

Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Douglas N Greve 


On 09/12/2017 09:06 AM, Benjamin Luerweg wrote:
> dear mr. Greve,
> dear fs community,
>
> first of all thank you very much for helping me so far.
>
> what i don’t understand is the difference between the value *CSF* 
> (within the aseg.stat) and the *CSFVol* which shows up inside
> the console while processing the command to generate the aseg.stat file.
The "CSF" label is a small ROI of CSF that did not fit into any of the 
standard ventricle definitions. It is not well-named and creates confusion.
>
> additional to this i would like to know why some of this values 
> directly showing up inside the console are not included/part of the 
> final aseg.stat?!
> is there a different way to get a file which includes this 
> morphometric data?
> (because like i told you: for example the aseg.stat value CSF differs 
> from the inside the console shown value CSFVol (which is not part of 
> aseg))
There is not a way to get the data from the console. However, you can 
compute *BrainSeg-**BrainSegNotVent to get venticular CSF volume
*
>
> regarding to this ratio which i need its the *VBR* i meant 
> (https://en.wikipedia.org/wiki/Ventricular-brain_ratio)
> whats the *best way to calculate this value?* which parameters should 
> i use?
Not sure. I guess it would be CSFVol/BrainSeg or CSFVol/BrainSegNotVent
>
> my last question is about how to calculate the whole corpus calosum 
> volume - is it possible to add all CC values to a value for the 
> complete CC?
I'm not sure that CC "volume" is meaningful since the CC is not really a 
3D structure. Maybe you want to use CC surface area?
>
>
> thank your very much in advance,
> benjamin luerweg
>
> _
>
>
>
>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve 
>> >:
>>
>>
>>
>> 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
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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.
>>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Benjamin Luerweg 
dear mr. Greve,
dear fs community,

first of all thank you very much for helping me so far.

what i don’t understand is the difference between the value CSF (within the 
aseg.stat) and the CSFVol which shows up inside 
the console while processing the command to generate the aseg.stat file.

additional to this i would like to know why some of this values directly 
showing up inside the console are not included/part of the final aseg.stat?!
is there a different way to get a file which includes this morphometric data? 
(because like i told you: for example the aseg.stat value CSF differs from the 
inside the console shown value CSFVol (which is not part of aseg))

regarding to this ratio which i need its the VBR i meant 
(https://en.wikipedia.org/wiki/Ventricular-brain_ratio 
)
whats the best way to calculate this value? which parameters should i use?

my last question is about how to calculate the whole corpus calosum volume - is 
it possible to add all CC values to a value for the complete CC?


thank your very much in advance,
benjamin luerweg

_



> Am 11.09.2017 um 22:01 schrieb Douglas N Greve :
> 
> 
> 
> 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
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> 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.
> 



___
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.

Re: [Freesurfer] labels used by freesurfer

2017-09-11 Thread Douglas N Greve 


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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.