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?
CSFVol why is this volume differing to the one within the segstat file?
and finally i would really love to know how to calculate a correct brain to liquor ratio?!
kind regards, ben
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
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 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 greve@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
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 greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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
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 greve@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
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 greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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
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 greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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 greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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 Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. >
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@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 > <greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>> <greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 >> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. 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dear guys
following the complete aseg numbers of one subject:
Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-White-Matter Left-Cerebellum-Cortex Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum 3rd-Ventricle 4th-Ventricle Brain-Stem Left-Hippocampus Left-Amygdala CSF Left-Accumbens-area Left-VentralDC Left-vessel Left-choroid-plexus Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-Cerebellum-White-Matter Right-Cerebellum-Cortex Right-Thalamus-Proper Right-Caudate Right-Putamen Right-Pallidum Right-Hippocampus Right-Amygdala Right-Accumbens-area Right-VentralDC Right-vessel Right-choroid-plexus 5th-Ventricle WM-hypointensities Left-WM-hypointensities Right-WM-hypointensities non-WM-hypointensities Left-non-WM-hypointensities Right-non-WM-hypointensities Optic-Chiasm CC_Posterior CC_Mid_Posterior CC_Central CC_Mid_Anterior CC_Anterior BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf lhCortexVol rhCortexVol CortexVol lhCerebralWhiteMatterVol rhCerebralWhiteMatterVol CerebralWhiteMatterVol SubCortGrayVol TotalGrayVol SupraTentorialVol SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles EstimatedTotalIntraCranialVol 8809.0 136.4 15122.6 57009.5 7385.8 4323.0 5072.5 2013.2 1089.2 2056.2 18473.3 3881.3 1582.9 1372.6 542.0 3924.7 40.9 391.0 7891.9 133.2 14079.5 58792.8 7741.6 4385.1 5131.0 1836.9 3926.7 1587.9 568.9 3780.6 5.3 473.2 0.0 645.9 0.0 0.0 0.0 0.0 0.0 261.6 905.0 518.5 508.6 492.6 760.5 1126369.0 1104587.0 1104465.35488 241058.315137 240689.144139 481747.459276 209640.844794 208308.050808 417948.895602 59222.0 658937.459276 979387.354878 962093.354878 958876.0 1588784.0 0.766102 1.080615 21.0 22.0 43.0 1470259.49914
as you can see brainsegvol and brainsegvolnotvent are really much bigger than left and right ventricles..
BrainSegVol BrainSegVolNotVent 1126369.0 1104587.0
Left-Lateral-Ventricle
Right-Lateral-Ventricle 8809.0
7891.9
calculating the value for the complete ventricle system using one of the two methods put out different values as described before..
any idea whats wrong about that? ..or how to correct it?
kind regards b
Am 18.09.2017 um 00:08 schrieb Douglas Greve greve@nmr.mgh.harvard.edu:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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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 greve@nmr.mgh.harvard.edu:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. 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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 Luerweg@students.uni-marburg.de:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. 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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 <Luerweg@students.uni-marburg.de mailto:Luerweg@students.uni-marburg.de>:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 > <Luerweg@students.uni-marburg.de > mailto:Luerweg@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 >> <greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>> <greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>> <greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 >>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto: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. 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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 greve@nmr.mgh.harvard.edu:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@students.uni-marburg.de>:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
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 >> <Luerweg@students.uni-marburg.de >> mailto:Luerweg@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 >>> <greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>> <greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>>> <greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto: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. 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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 greve@nmr.mgh.harvard.edu:
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 <Luerweg@students.uni-marburg.de mailto:Luerweg@students.uni-marburg.de>:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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 20115,899999999998 (second calculation) any ideas why the difference is that big?
kind regards
> Am 17.09.2017 um 20:51 schrieb Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: > > 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 >>> <Luerweg@students.uni-marburg.de >>> mailto:Luerweg@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 >>>> <greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>> <greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>>>> <greve@nmr.mgh.harvard.edu >>>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@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 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve@nmr.mgh.harvard.edu >>>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>> <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto: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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Benjamin Luerweg -
Bruce Fischl -
Douglas Greve -
Douglas N Greve