Doug and Bruce. Many thousands of thanks
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: Thursday, November 06, 2014 12:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume
On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote:
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the statistics at the end of there running and we can check the results in aseg.stats (the output of recon-all) and fa.stats (the output of dt-recon for FA).
In those files we have the white matter volume for many different parts of the brain like the right and left cerebral white matter.
If we check the volumes in those files we can see that we have differences between the numbers and I can explain that by the following: in aseg.stats the white matter volume is derived from the T1 segmentation in the structural space and in fa.stats the white matter volume is derived from the FA map in diffusion space and the difference between the volumes is the difference between the accuracy of the images in different spaces.
Almost. The value in aseg.stats is derived from the surfaces which is even more accurate than the 1mm space values (though they are pretty close).
Now:
- If we want to study the relationship between the FA and the right
hemispheric white matter volume for example, we should not care about the volumes in fa.stasts because it is not accurate?!
I would use the value from the aseg.stats file. I would not say that the value from fa.stats is not accurate, it is just not as accurate as the surface-based measure.
in this case what is the optimal and correct method in freeSurfer to do such like this comparison, is it by moving the FA map to the structural space by registering the FA map to T1 or by using the volumes in aseg.stats and the metrics values from fa.stats? or we can use the fa values and the volumes from fa.stats?
Use the value from the aseg.stats
2.What is the exact usage for the volumes mentioned in FA.stats
They may or may not be used for anything. They are just values that are recorded by the program.
- What is the meaning and the exact usage of min-max intensity range
(intensity of what) in aseg.stats and fa.stats
The min is the minimum value of the intensity (norm.mgz or fa.nii) in the ROI, max is the maximum. Again, they may or may not be used for anything. They are just values that are recorded by the program.
doug
So Sorry for this long email but as always I am looking forward to learn from you
Thanks
Mohamad
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