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