Re: [Freesurfer] license error
Beside that I recognised that some issues with the license file are based on the following aspect: While running freesurfer on Mac OS it Didn't work for me creating the license file under Mac OS itself. I realised that after creating the file under windows 10 and copying that file back to mac freesurfer started without an error. Kind regards, B. Luerweg _ Benjamin Luerweg Deutschhausstraße 8 35037 Marburg 0049 1575 444 14 14 > Am 14.09.2017 um 11:57 schrieb Ritesh Mahajan <ritesh.maha...@ripl.ricoh.com>: > > Hello team, > > I created the license.txt at location FREESURFER_HOME and pasted the lines > sent to me after registration. Still i find the following errors. > > "ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment" > > Thanks, > Ritesh Mahajan > ___ > 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.
[Freesurfer] how to get the volume of the complete ventricle system ?
dear all, Ive tried to get the volume of the ventricle system by using two different calculations. first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent than i tried to simply add all the seprate parts of the ventricle system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle) after doing this i realized that the two values were differing like -> 217820,00 (first calculation) and 20115,8998 (second calculation) any ideas why the difference is that big? kind regards ___ 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
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 <gr...@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 20115,8998 (second calculation) >> any ideas why the difference is that big? >> >> >> kind regards >> >> >> >>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fis...@nmr.mgh.harvard.edu >>> <mailto:fis...@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 >>>>> <luer...@students.uni-marburg.de >>>>> <mailto:luer...@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 >>>>>> <gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>>: >>>>>> >>>
Re: [Freesurfer] labels used by freesurfer
>>>> 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 > <luer...@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 <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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 20115,8998 (second calculation) >>> any ideas why the difference is that big? >>> >>> >>> kind regards >>> >>> >>> >>>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fis...@nmr.mgh.harvard.edu >>>> <mailto:fis...@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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>
Re: [Freesurfer] labels used by freesurfer
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 <gr...@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 >>> <luer...@students.uni-marburg.de >>> <mailto:luer...@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 >>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 20115,8998 (second >>>>> calculation) >>>>> any ideas why the difference is that big? >>>>> >>>>> >>>>> kind regards >>>>> >>>>> >>>>> >>>>>> Am 17.09.2017 um 20:51 schrieb Bruce Fischl >>>>>> <fis...@nmr.mgh.harvard.edu <mailto:fis...@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 comm
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
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 > <luer...@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 <gr...@nmr.mgh.harvard.edu >> <mailto: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, >>>>> &g
Re: [Freesurfer] labels used by freesurfer
alright.. so far…BUT: Ive tried to get the volume of the ventricle system by using two different calculations. first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent than i tried to simply add all the seprate parts of the ventricle system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle) after doing this i realized that the two values were differing like -> 217820,00 (first calculation) and 20115,8998 (second calculation) any ideas why the difference is that big? kind regards > Am 17.09.2017 um 20:51 schrieb Bruce Fischl <fis...@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 >>> <luer...@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 <gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>>>: >>>> >>>> >>>> >>>> On 09/13/2017 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
[Freesurfer] what does the CSF label describe?
dear all, i already 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, b. luerweg doctoral student___ 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
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 - >>>&
[Freesurfer] adding volumes of seperated parts of one structure?
dear all, 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? kind regards, ben luerweg ___ 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.
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
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.
[Freesurfer] Choroid plexus analysis
External Email - Use Caution Dear community, anyone out there who can give me some information regarding how valid a volume detection of the choroid plexus is? I used fs 6.0. Kind regards, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
