yes. Partial volume correction helps both accuracy and repeatability. You can certainly use our (partial-volume) corrected WM volumes and the FA from FSL if you want
cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: > Hi Bruce, > Actually I am totally confused and this is the reason for my question! > What is the best and trusted approach in this case? > I want to study the relationship between the FA and the right and left > hemispheric white matter. I generated the DTI metrics and volume using FSL. I > am sure that the calculated white matter volume in FSL is not correct because > it is closer to what I am thinking about. > in this case can I use and is it valid if I use the volume from the output of > Freesurfer and the metrics from FSL in my analsysis? > > Thanks > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, October 31, 2014 11:35 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] White matter volume > > Hi Mohamad > > this is probably due to the partial-volume correction that we typically > compute when we estimate volumes in the stats files. > > cheers > Bruce > On Fri, 31 Oct 2014, > Alshikho, Mohamad J. wrote: > >> Thanks Doug, >> In order to improve my understanding for the analysis that I am working on >> and in the process of my learning I am tring to calculate the volume in many >> different ways. Actually It is very easy, simple and possible to use the >> numbers mentioned in aseg.stats but what if we got different results when we >> use different methods? >> I caclated the right and left hemispheric white matter volume in FSL using a >> mask deriverd from the T1 segmentation in Freesurfer "lh.dwhite.mgz , >> rh.dwhite.mgz" then I binarized those masks and I registered them to my T1 >> then I used the command line "fslstats <T1> -k my mask -V" What surprised >> me is that the volume was totally different from the one mentioned in >> aseg.stats (attached) >> >> I highly appreciate any advice. >> looking forward to learn from you >> Mohamad >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, October 31, 2014 11:04 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] White matter volume >> >> I would suggest using the value in aseg.stats. Is that not possible? >> >> On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: >>> Thanks Doug! >>> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of >>> mris_volmask? >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Friday, October 31, 2014 10:02 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] White matter volume >>> >>> The aseg is not surface-based and will not be as accurate >>> doug >>> >>> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: >>>> Hi Bruce, >>>> I wanted to calculate the right and left hemispheric white matter >>>> volume using a mask. >>>> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the >>>> outputs of mris_volmmask after binarize them) and the right and left >>>> hemispheric white matter masks from aseg.mgz atlas (the output of >>>> mri_binarize command line)? >>>> I am asking this question because those masks gave me different >>>> estimation for the volume? >>>> >>>> Thanks! >>>> Mohamad >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer 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. 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