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 The information in this e-mail is intended only for the person to whom it is addressed. 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