Re: [Freesurfer] labels used by freesurfer
f the voxels. >>>>>>>>>>> so my questions again:what is the label CSF (aseg.stats) >>>>>>>>>>> describing? >>>>>>>>>>> and what does it stands for? cer.spinal.fluid? >>>>>>>>>>> what is the label CSFVol (console) describing? and what does >>>>>>>>>>> it stands >>>>>>>>>>> for if the CSF label is a volume already? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I’ve been trying to understand the meaning of the CSF (index24) by >>>>>>>>>>> using freeviewer.. but no chance… for me it seems to be not >>>>>>>>>>> part of >>>>>>>>>>> the ventricle system as i know it? maybe you can describe it >>>>>>>>>>> using an >>>>>>>>>>> image? >>>>>>>>>> Not sure. This was a label supplied to us by the center for >>>>>>>>>> morphometric >>>>>>>>>> analysis (CMA) about 20 years ago, and I can't find the docs on >>>>>>>>>> it. It >>>>>>>>>> does not appear to be part of the ventricular system. I think >>>>>>>>>> it must be >>>>>>>>>> some kind of of sulcal csf in the midline. I don't know why the CMA >>>>>>>>>> decided to label that and not other sulcal CSF. It is pretty >>>>>>>>>> small and >>>>>>>>>> probably will not affect your calculations that much either way >>>>>>>>>>> beside that: whats the advantage of this two lables beside >>>>>>>>>>> getting the >>>>>>>>>>> whole ventricle volume by adding ventricles (lateral,inferior >>>>>>>>>>> lateral, >>>>>>>>>>> 3rd, 4th, 5th)? >>>>>>>>>> I don't understand what you mean. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> *REGARDING CC (corpus callosum):* >>>>>>>>>>> >>>>>>>>>>> why do you think that the corpus callosum is not a 3D body? of >>>>>>>>>>> cause >>>>>>>>>>> it is or what did you mean? >>>>>>>>>>> setting the CC parts in free viewer it seems as if it >>>>>>>>>>> shouldn’t be a >>>>>>>>>>> big deal to add the separated parts of the CC to one value?! >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> kind regards, >>>>>>>>>>> benjamin luerweg >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> doctoral student >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve >>>>>>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>>>>>>>>> >>>>>>>>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>>>>>>>> >>>>>>>>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles >>>>>>>>>>>> plus the CSF >>>>>>>>>>>> label >>>>>>>>>>>> >>>>>>>>>>>> VentChorVol is the volume of choroird plexus, lateral >>>>>>>>>>>> ventricles, and >>>>>>>>>>>> inferior lateral ventricles >>>>>>>>>>>> >>>>>>>>>>>> BrainSegVolNotVent =
Re: [Freesurfer] labels used by freesurfer
> using freeviewer.. but no chance… for me it seems to be not >>>>>>>>>> part of >>>>>>>>>> the ventricle system as i know it? maybe you can describe it >>>>>>>>>> using an >>>>>>>>>> image? >>>>>>>>> Not sure. This was a label supplied to us by the center for >>>>>>>>> morphometric >>>>>>>>> analysis (CMA) about 20 years ago, and I can't find the docs on >>>>>>>>> it. It >>>>>>>>> does not appear to be part of the ventricular system. I think >>>>>>>>> it must be >>>>>>>>> some kind of of sulcal csf in the midline. I don't know why the CMA >>>>>>>>> decided to label that and not other sulcal CSF. It is pretty >>>>>>>>> small and >>>>>>>>> probably will not affect your calculations that much either way >>>>>>>>>> >>>>>>>>>> beside that: whats the advantage of this two lables beside >>>>>>>>>> getting the >>>>>>>>>> whole ventricle volume by adding ventricles (lateral,inferior >>>>>>>>>> lateral, >>>>>>>>>> 3rd, 4th, 5th)? >>>>>>>>> I don't understand what you mean. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *REGARDING CC (corpus callosum):* >>>>>>>>>> >>>>>>>>>> why do you think that the corpus callosum is not a 3D body? of >>>>>>>>>> cause >>>>>>>>>> it is or what did you mean? >>>>>>>>>> setting the CC parts in free viewer it seems as if it >>>>>>>>>> shouldn’t be a >>>>>>>>>> big deal to add the separated parts of the CC to one value?! >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> kind regards, >>>>>>>>>> benjamin luerweg >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> doctoral student >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve >>>>>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>>>>>>>> >>>>>>>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>>>>>>> >>>>>>>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles >>>>>>>>>>> plus the CSF >>>>>>>>>>> label >>>>>>>>>>> >>>>>>>>>>> VentChorVol is the volume of choroird plexus, lateral >>>>>>>>>>> ventricles, and >>>>>>>>>>> inferior lateral ventricles >>>>>>>>>>> >>>>>>>>>>> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >>>>>>>>>>>> Hey Mr. Greve, >>>>>>>>>>>> >>>>>>>>>>>> thank your very much again! >>>>>>>>>>>> if i understand you right, the inside the console shown up >>>>>>>>>>>> values >>>>>>>>>>>> can’t be extracted into a separate file? >>>>>>>>>>>> >>>>>>>>>>>> beside that, this values are of interest for me, so that i &
Re: [Freesurfer] labels used by freesurfer
t your calculations that much either way >>>>>>>>> >>>>>>>>> beside that: whats the advantage of this two lables beside >>>>>>>>> getting the >>>>>>>>> whole ventricle volume by adding ventricles (lateral,inferior >>>>>>>>> lateral, >>>>>>>>> 3rd, 4th, 5th)? >>>>>>>> I don't understand what you mean. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> *REGARDING CC (corpus callosum):* >>>>>>>>> >>>>>>>>> why do you think that the corpus callosum is not a 3D body? of >>>>>>>>> cause >>>>>>>>> it is or what did you mean? >>>>>>>>> setting the CC parts in free viewer it seems as if it >>>>>>>>> shouldn’t be a >>>>>>>>> big deal to add the separated parts of the CC to one value?! >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> kind regards, >>>>>>>>> benjamin luerweg >>>>>>>>> >>>>>>>>> >>>>>>>>> doctoral student >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve >>>>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>>>>>>> >>>>>>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>>>>>> >>>>>>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles >>>>>>>>>> plus the CSF >>>>>>>>>> label >>>>>>>>>> >>>>>>>>>> VentChorVol is the volume of choroird plexus, lateral >>>>>>>>>> ventricles, and >>>>>>>>>> inferior lateral ventricles >>>>>>>>>> >>>>>>>>>> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >>>>>>>>>>> Hey Mr. Greve, >>>>>>>>>>> >>>>>>>>>>> thank your very much again! >>>>>>>>>>> if i understand you right, the inside the console shown up >>>>>>>>>>> values >>>>>>>>>>> can’t be extracted into a separate file? >>>>>>>>>>> >>>>>>>>>>> beside that, this values are of interest for me, so that i >>>>>>>>>>> copied them >>>>>>>>>>> to a text file. >>>>>>>>>>> as you can see:Getting Brain Volume Statistics >>>>>>>>>>> ... >>>>>>>>>>> SubCortGMVol 56306.000 >>>>>>>>>>> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >>>>>>>>>>> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 >>>>>>>>>>> pctdiff=0.352 >>>>>>>>>>> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 >>>>>>>>>>> pctdiff=0.231 >>>>>>>>>>> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 >>>>>>>>>>> pctdiff=0.034 >>>>>>>>>>> BrainSegVolNotVent 1082437.000 >>>>>>>>>>> CerebellumVol 145310.000 >>>>>>>>>>> VentChorVol 23535.000 >>>>>>>>>>> 3rd4th5thCSF 3528.000 >>>>>>>>>>> CSFVol 963.000, >>>>>>>>>>> OptChiasmVol 154.000 >&g
Re: [Freesurfer] labels used by freesurfer
gt;>>>>>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve >>>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>>: >>>>>>>>> >>>>>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>>>>> >>>>>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the >>>>>>>>> CSF >>>>>>>>> label >>>>>>>>> >>>>>>>>> VentChorVol is the volume of choroird plexus, lateral ventricles, and >>>>>>>>> inferior lateral ventricles >>>>>>>>> >>>>>>>>> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >>>>>>>>>> Hey Mr. Greve, >>>>>>>>>> >>>>>>>>>> thank your very much again! >>>>>>>>>> if i understand you right, the inside the console shown up values >>>>>>>>>> can’t be extracted into a separate file? >>>>>>>>>> >>>>>>>>>> beside that, this values are of interest for me, so that i copied >>>>>>>>>> them >>>>>>>>>> to a text file. >>>>>>>>>> as you can see:Getting Brain Volume Statistics >>>>>>>>>> ... >>>>>>>>>> SubCortGMVol 56306.000 >>>>>>>>>> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >>>>>>>>>> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 >>>>>>>>>> pctdiff=0.352 >>>>>>>>>> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 >>>>>>>>>> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 >>>>>>>>>> pctdiff=0.034 >>>>>>>>>> BrainSegVolNotVent 1082437.000 >>>>>>>>>> CerebellumVol 145310.000 >>>>>>>>>> VentChorVol 23535.000 >>>>>>>>>> 3rd4th5thCSF 3528.000 >>>>>>>>>> CSFVol 963.000, >>>>>>>>>> OptChiasmVol 154.000 >>>>>>>>>> MaskVol 1526326.000 >>>>>>>>>> >>>>>>>>>> am i right that this CSFVol is the Volume of all ventricles not >>>>>>>>>> including >>>>>>>>>> the extra cerebral CSF? >>>>>>>>>> i tried to calculate the CSFVol reverse by calculating: VentChorVol - >>>>>>>>>> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >>>>>>>>>> >>>>>>>>>> and what exactly is the VentChorVol and 3rd4th5thCSF for? >>>>>>>>>> >>>>>>>>>> im a bit confused about all this lables and im sorry for asking you >>>>>>>>>> so >>>>>>>>>> much but i would really appreciate to solve this pity situation. >>>>>>>>>> >>>>>>>>>> do you have a kind of an overview? >>>>>>>>>> >>>>>>>>>> thank you in advance again, >>>>>>>>>> >>>>>>>>>> ben luerweg >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >>>>>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:gr..
Re: [Freesurfer] labels used by 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 >>>>>>>> <gr...@nmr.mgh.harvard.edu >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>>: >>>>>>>> >>>>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>>>> >>>>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF >>>>>>>> label >>>>>>>> >>>>>>>> VentChorVol is the volume of choroird plexus, lateral ventricles, and >>>>>>>> inferior lateral ventricles >>>>>>>> >>>>>>>> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 09/12/2
Re: [Freesurfer] labels used by freesurfer
tricles plus the CSF label VentChorVol is the volume of choroird plexus, lateral ventricles, and inferior lateral ventricles BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: Hey Mr. Greve, thank your very much again! if i understand you right, the inside the console shown up values can’t be extracted into a separate file? beside that, this values are of interest for me, so that i copied them to a text file. as you can see:Getting Brain Volume Statistics ... SubCortGMVol 56306.000 SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 BrainSegVolNotVent 1082437.000 CerebellumVol 145310.000 VentChorVol 23535.000 3rd4th5thCSF 3528.000 CSFVol 963.000, OptChiasmVol 154.000 MaskVol 1526326.000 am i right that this CSFVol is the Volume of all ventricles not including the extra cerebral CSF? i tried to calculate the CSFVol reverse by calculating: VentChorVol - Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? and what exactly is the VentChorVol and 3rd4th5thCSF for? im a bit confused about all this lables and im sorry for asking you so much but i would really appreciate to solve this pity situation. do you have a kind of an overview? thank you in advance again, ben luerweg Am 11.09.2017 um 22:01 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>>: On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: dear fs community, as a kind of a freesurfer greenhorn i would kindly ask you to help me out with identifying the different labels used by freesurfer. after using mri segstats most of the labels seem to be describing thereselfs in proper way. what i don’t understand are for example the different volume values showing up inside the console after entering the segstat command. VentChorVol what does this label explain? Volume of all ventricles plus the volume of the chorioid plexus. CSFVolwhy is this volume differing to the one within the segstat file? Volume of all ventricles (not well named because it does not include extra cerebral CSF) and finally i would really love to know how to calculate a correct brain to liquor ratio?! Do you mean brain volume to total CSF volume? See above kind regards, ben ___ 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>> 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 gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@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>> 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<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<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 w
Re: [Freesurfer] labels used by freesurfer
sulcal CSF. It is pretty small and >>>> probably will not affect your calculations that much either way >>>>> >>>>> beside that: whats the advantage of this two lables beside getting the >>>>> whole ventricle volume by adding ventricles (lateral,inferior lateral, >>>>> 3rd, 4th, 5th)? >>>> I don't understand what you mean. >>>>> >>>>> >>>>> >>>>> *REGARDING CC (corpus callosum):* >>>>> >>>>> why do you think that the corpus callosum is not a 3D body? of cause >>>>> it is or what did you mean? >>>>> setting the CC parts in free viewer it seems as if it shouldn’t be a >>>>> big deal to add the separated parts of the CC to one value?! >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> kind regards, >>>>> benjamin luerweg >>>>> >>>>> >>>>> doctoral student >>>>> >>>>> >>>>> >>>>> >>>>>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve >>>>>> <gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>>: >>>>>> >>>>>> CSFVol is actually the volume of the CSF label (index 24) >>>>>> >>>>>> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF >>>>>> label >>>>>> >>>>>> VentChorVol is the volume of choroird plexus, lateral ventricles, and >>>>>> inferior lateral ventricles >>>>>> >>>>>> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >>>>>> >>>>>> >>>>>> >>>>>> On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >>>>>>> Hey Mr. Greve, >>>>>>> >>>>>>> thank your very much again! >>>>>>> if i understand you right, the inside the console shown up values >>>>>>> can’t be extracted into a separate file? >>>>>>> >>>>>>> beside that, this values are of interest for me, so that i copied them >>>>>>> to a text file. >>>>>>> as you can see:Getting Brain Volume Statistics >>>>>>> ... >>>>>>> SubCortGMVol 56306.000 >>>>>>> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >>>>>>> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 >>>>>>> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 >>>>>>> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 >>>>>>> BrainSegVolNotVent 1082437.000 >>>>>>> CerebellumVol 145310.000 >>>>>>> VentChorVol 23535.000 >>>>>>> 3rd4th5thCSF 3528.000 >>>>>>> CSFVol 963.000, >>>>>>> OptChiasmVol 154.000 >>>>>>> MaskVol 1526326.000 >>>>>>> >>>>>>> am i right that this CSFVol is the Volume of all ventricles not >>>>>>> including >>>>>>> the extra cerebral CSF? >>>>>>> i tried to calculate the CSFVol reverse by calculating: VentChorVol - >>>>>>> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >>>>>>> >>>>>>> and what exactly is the VentChorVol and 3rd4th5thCSF for? >>>>>>> >>>>>>> im a bit confused about all this lables and im sorry for asking you so >>>>>>> much but i would really appreciate to solve this pity situation. >>>>>>> >>>>>>> do you have a kind of an overview? >>>>>>> >>>>>>> thank you in advance again, >>>>>>> >>>>>>> ben luerweg >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >
Re: [Freesurfer] labels used by freesurfer
0 am i right that this CSFVol is the Volume of all ventricles not including the extra cerebral CSF? i tried to calculate the CSFVol reverse by calculating: VentChorVol - Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? and what exactly is the VentChorVol and 3rd4th5thCSF for? im a bit confused about all this lables and im sorry for asking you so much but i would really appreciate to solve this pity situation. do you have a kind of an overview? thank you in advance again, ben luerweg Am 11.09.2017 um 22:01 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>: On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: dear fs community, as a kind of a freesurfer greenhorn i would kindly ask you to help me out with identifying the different labels used by freesurfer. after using mri segstats most of the labels seem to be describing thereselfs in proper way. what i don’t understand are for example the different volume values showing up inside the console after entering the segstat command. VentChorVol what does this label explain? Volume of all ventricles plus the volume of the chorioid plexus. CSFVolwhy is this volume differing to the one within the segstat file? Volume of all ventricles (not well named because it does not include extra cerebral CSF) and finally i would really love to know how to calculate a correct brain to liquor ratio?! Do you mean brain volume to total CSF volume? See above kind regards, ben ___ 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 gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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. ___ 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 gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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.harv
Re: [Freesurfer] labels used by freesurfer
t;>>>> thank your very much again! >>>>> if i understand you right, the inside the console shown up values >>>>> can’t be extracted into a separate file? >>>>> >>>>> beside that, this values are of interest for me, so that i copied them >>>>> to a text file. >>>>> as you can see:Getting Brain Volume Statistics >>>>> ... >>>>> SubCortGMVol 56306.000 >>>>> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >>>>> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 >>>>> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 >>>>> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 >>>>> BrainSegVolNotVent 1082437.000 >>>>> CerebellumVol 145310.000 >>>>> VentChorVol 23535.000 >>>>> 3rd4th5thCSF 3528.000 >>>>> CSFVol 963.000, >>>>> OptChiasmVol 154.000 >>>>> MaskVol 1526326.000 >>>>> >>>>> am i right that this CSFVol is the Volume of all ventricles not >>>>> including >>>>> the extra cerebral CSF? >>>>> i tried to calculate the CSFVol reverse by calculating: VentChorVol - >>>>> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >>>>> >>>>> and what exactly is the VentChorVol and 3rd4th5thCSF for? >>>>> >>>>> im a bit confused about all this lables and im sorry for asking you so >>>>> much but i would really appreciate to solve this pity situation. >>>>> >>>>> do you have a kind of an overview? >>>>> >>>>> thank you in advance again, >>>>> >>>>> ben luerweg >>>>> >>>>> >>>>> >>>>>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>>> >>>>>> >>>>>> >>>>>> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >>>>>>> dear fs community, >>>>>>> >>>>>>> as a kind of a freesurfer greenhorn i would kindly ask you to help me >>>>>>> out with identifying the different labels used by freesurfer. >>>>>>> after using mri segstats most of the labels seem to be describing >>>>>>> thereselfs in proper way. >>>>>>> >>>>>>> what i don’t understand are for example the different volume values >>>>>>> showing up inside the console after entering the segstat command. >>>>>>> >>>>>>> VentChorVol what does this label explain? >>>>>> Volume of all ventricles plus the volume of the chorioid plexus. >>>>>>> >>>>>>> CSFVolwhy is this volume differing to the one within the segstat file? >>>>>> Volume of all ventricles (not well named because it does not include >>>>>> extra cerebral CSF) >>>>>>> >>>>>>> and finally i would really love to know how to calculate a correct >>>>>>> brain to liquor ratio?! >>>>>> Do you mean brain volume to total CSF volume? See above >>>>>>> >>>>>>> >>>>>>> kind regards, >>>>>>> ben >>>>>>> >>>>>>> >>>>>>> ___ >>>>>>> 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> >>>>>> >>>>>> -- >>>>>>
Re: [Freesurfer] labels used by freesurfer
gt; Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >>>> >>>> and what exactly is the VentChorVol and 3rd4th5thCSF for? >>>> >>>> im a bit confused about all this lables and im sorry for asking you so >>>> much but i would really appreciate to solve this pity situation. >>>> >>>> do you have a kind of an overview? >>>> >>>> thank you in advance again, >>>> >>>> ben luerweg >>>> >>>> >>>> >>>>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>> >>>>> >>>>> >>>>> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >>>>>> dear fs community, >>>>>> >>>>>> as a kind of a freesurfer greenhorn i would kindly ask you to help me >>>>>> out with identifying the different labels used by freesurfer. >>>>>> after using mri segstats most of the labels seem to be describing >>>>>> thereselfs in proper way. >>>>>> >>>>>> what i don’t understand are for example the different volume values >>>>>> showing up inside the console after entering the segstat command. >>>>>> >>>>>> VentChorVol what does this label explain? >>>>> Volume of all ventricles plus the volume of the chorioid plexus. >>>>>> >>>>>> CSFVolwhy is this volume differing to the one within the segstat file? >>>>> Volume of all ventricles (not well named because it does not include >>>>> extra cerebral CSF) >>>>>> >>>>>> and finally i would really love to know how to calculate a correct >>>>>> brain to liquor ratio?! >>>>> Do you mean brain volume to total CSF volume? See above >>>>>> >>>>>> >>>>>> kind regards, >>>>>> ben >>>>>> >>>>>> >>>>>> ___ >>>>>> 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 >>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>>> 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 >>>>> <ma
Re: [Freesurfer] labels used by 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 >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>: >> >> CSFVol is actually the volume of the CSF label (index 24) >> >> 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF >> label >> >> VentChorVol is the volume of choroird plexus, lateral ventricles, and >> inferior lateral ventricles >> >> BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; >> >> >> >> On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >>> Hey Mr. Greve, >>> >>> thank your very much again! >>> if i understand you right, the inside the console shown up values >>> can’t be extracted into a separate file? >>> >>> beside that, this values are of interest for me, so that i copied them >>> to a text file. >>> as you can see:Getting Brain Volume Statistics >>> ... >>> SubCortGMVol 56306.000 >>> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >>> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 >>> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 >>> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 >>> BrainSegVolNotVent 1082437.000 >>> CerebellumVol 145310.000 >>> VentChorVol 23535.000 >>> 3rd4th5thCSF 3528.000 >>> CSFVol 963.000, >>> OptChiasmVol 154.000 >>> MaskVol 1526326.000 >>> >>> am i right that this CSFVol is the Volume of all ventricles not >>> including >>> the extra cerebral CSF? >>> i tried to calculate the CSFVol reverse by calculating: VentChorVol - >>> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >>> >>> and what exactly is the VentChorVol and 3rd4th5thCSF for? >>> >>> im a bit confused about all this lables and im sorry for asking you so >>> much but i would really appreciate to solve this pity situation. >>> >>> do you have a kind of an overview? >>> >>> thank you in advance again, >>> >>> ben luerweg >>> >>> >>> >>>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >>>> <gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>>: >>>> >>>> >>>> >>>> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >>>>> dear fs community, >>>>> >>>>>
Re: [Freesurfer] labels used by 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 <gr...@nmr.mgh.harvard.edu>: > > CSFVol is actually the volume of the CSF label (index 24) > > 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF > label > > VentChorVol is the volume of choroird plexus, lateral ventricles, and > inferior lateral ventricles > > BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; > > > > On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: >> Hey Mr. Greve, >> >> thank your very much again! >> if i understand you right, the inside the console shown up values >> can’t be extracted into a separate file? >> >> beside that, this values are of interest for me, so that i copied them >> to a text file. >> as you can see:Getting Brain Volume Statistics >> ... >> SubCortGMVol 56306.000 >> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 >> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 >> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 >> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 >> BrainSegVolNotVent 1082437.000 >> CerebellumVol 145310.000 >> VentChorVol 23535.000 >> 3rd4th5thCSF 3528.000 >> CSFVol 963.000, >> OptChiasmVol 154.000 >> MaskVol 1526326.000 >> >> am i right that this CSFVol is the Volume of all ventricles not including >> the extra cerebral CSF? >> i tried to calculate the CSFVol reverse by calculating: VentChorVol - >> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? >> >> and what exactly is the VentChorVol and 3rd4th5thCSF for? >> >> im a bit confused about all this lables and im sorry for asking you so >> much but i would really appreciate to solve this pity situation. >> >> do you have a kind of an overview? >> >> thank you in advance again, >> >> ben luerweg >> >> >> >>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>: >>> >>> >>> >>> 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 >>>> >>>> >>>> ki
Re: [Freesurfer] labels used by freesurfer
CSFVol is actually the volume of the CSF label (index 24) 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF label VentChorVol is the volume of choroird plexus, lateral ventricles, and inferior lateral ventricles BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ; On 09/12/2017 02:13 PM, Benjamin Luerweg wrote: > Hey Mr. Greve, > > thank your very much again! > if i understand you right, the inside the console shown up values > can’t be extracted into a separate file? > > beside that, this values are of interest for me, so that i copied them > to a text file. > as you can see:Getting Brain Volume Statistics > ... > SubCortGMVol 56306.000 > SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 > SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 > BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 > BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 > BrainSegVolNotVent 1082437.000 > CerebellumVol 145310.000 > VentChorVol 23535.000 > 3rd4th5thCSF 3528.000 > CSFVol 963.000, > OptChiasmVol 154.000 > MaskVol 1526326.000 > > am i right that this CSFVol is the Volume of all ventricles not including > the extra cerebral CSF? > i tried to calculate the CSFVol reverse by calculating: VentChorVol - > Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? > > and what exactly is the VentChorVol and 3rd4th5thCSF for? > > im a bit confused about all this lables and im sorry for asking you so > much but i would really appreciate to solve this pity situation. > > do you have a kind of an overview? > > thank you in advance again, > > ben luerweg > > > >> Am 11.09.2017 um 22:01 schrieb Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>: >> >> >> >> 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 >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels used by freesurfer
Hey Mr. Greve, thank your very much again! if i understand you right, the inside the console shown up values can’t be extracted into a separate file? beside that, this values are of interest for me, so that i copied them to a text file. as you can see: Getting Brain Volume Statistics ... SubCortGMVol 56306.000 SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343 SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352 BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231 BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034 BrainSegVolNotVent 1082437.000 CerebellumVol 145310.000 VentChorVol 23535.000 3rd4th5thCSF 3528.000 CSFVol 963.000, OptChiasmVol 154.000 MaskVol 1526326.000 am i right that this CSFVol is the Volume of all ventricles not including the extra cerebral CSF? i tried to calculate the CSFVol reverse by calculating: VentChorVol - Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this? and what exactly is the VentChorVol and 3rd4th5thCSF for? im a bit confused about all this lables and im sorry for asking you so much but i would really appreciate to solve this pity situation. do you have a kind of an overview? thank you in advance again, ben luerweg > Am 11.09.2017 um 22:01 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > > > On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >> dear fs community, >> >> as a kind of a freesurfer greenhorn i would kindly ask you to help me >> out with identifying the different labels used by freesurfer. >> after using mri segstats most of the labels seem to be describing >> thereselfs in proper way. >> >> what i don’t understand are for example the different volume values >> showing up inside the console after entering the segstat command. >> >> VentChorVol what does this label explain? > Volume of all ventricles plus the volume of the chorioid plexus. >> >> CSFVolwhy is this volume differing to the one within the segstat file? > Volume of all ventricles (not well named because it does not include > extra cerebral CSF) >> >> and finally i would really love to know how to calculate a correct >> brain to liquor ratio?! > Do you mean brain volume to total CSF volume? See above >> >> >> kind regards, >> ben >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labels used by freesurfer
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 >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>: >> >> >> >> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >>> dear fs community, >>> >>> as a kind of a freesurfer greenhorn i would kindly ask you to help me >>> out with identifying the different labels used by freesurfer. >>> after using mri segstats most of the labels seem to be describing >>> thereselfs in proper way. >>> >>> what i don’t understand are for example the different volume values >>> showing up inside the console after entering the segstat command. >>> >>> VentChorVol what does this label explain? >> Volume of all ventricles plus the volume of the chorioid plexus. >>> >>> CSFVolwhy is this volume differing to the one within the segstat file? >> Volume of all ventricles (not well named because it does not include >> extra cerebral CSF) >>> >>> and finally i would really love to know how to calculate a correct >>> brain to liquor ratio?! >> Do you mean brain volume to total CSF volume? See above >>> >>> >>> kind regards, >>> ben >>> >>> >>> ___ >>> 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 >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels used by freesurfer
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 <gr...@nmr.mgh.harvard.edu>: > > > > On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: >> dear fs community, >> >> as a kind of a freesurfer greenhorn i would kindly ask you to help me >> out with identifying the different labels used by freesurfer. >> after using mri segstats most of the labels seem to be describing >> thereselfs in proper way. >> >> what i don’t understand are for example the different volume values >> showing up inside the console after entering the segstat command. >> >> VentChorVol what does this label explain? > Volume of all ventricles plus the volume of the chorioid plexus. >> >> CSFVolwhy is this volume differing to the one within the segstat file? > Volume of all ventricles (not well named because it does not include > extra cerebral CSF) >> >> and finally i would really love to know how to calculate a correct >> brain to liquor ratio?! > Do you mean brain volume to total CSF volume? See above >> >> >> kind regards, >> ben >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labels used by freesurfer
On 09/11/2017 01:20 PM, Benjamin Luerweg wrote: > dear fs community, > > as a kind of a freesurfer greenhorn i would kindly ask you to help me > out with identifying the different labels used by freesurfer. > after using mri segstats most of the labels seem to be describing > thereselfs in proper way. > > what i don’t understand are for example the different volume values > showing up inside the console after entering the segstat command. > > VentChorVol what does this label explain? Volume of all ventricles plus the volume of the chorioid plexus. > > CSFVolwhy is this volume differing to the one within the segstat file? Volume of all ventricles (not well named because it does not include extra cerebral CSF) > > and finally i would really love to know how to calculate a correct > brain to liquor ratio?! Do you mean brain volume to total CSF volume? See above > > > kind regards, > ben > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] labels used by freesurfer
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___ 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.
