Thanks a lot!!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] White matter volume
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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 greve@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