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, >>>>> >>>>> 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> >>>>> 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> >>>> 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 >>>> 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/ >>>> >>>> _______________________________________________ >>>> 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 >> >> -- >> 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 >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- 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
