It is hard to say. As Anderson said, we have the improved method for
computing volume. But just because something is improved does not mean
that results will be more significant!
On 5/2/17 1:17 PM, John Anderson wrote:
Dear Doug,
Thank you very much for the clarification!! I highly appreciate your
science and help.
I received an answer about my question from your colleague Dr Anderson
Winkler (Below) who directed me to review the paper (link also bellow).
My last question is: can Freesurfer 6 address "better" the
relationship between volume and thickness. I mean if Free surfer 6
find results similar to FS5.3 (regarding thickness effect and no
volume effect between the groups), is this still be explained as noise?
regards,
John
"Hi John,
Thanks for the comments. Yes, it's possible. Thickness gives some
contribution to volume, but these two aren't the same and aren't
comparable. In fact, we and others have seen that the variability of
volume across subjects is better explained by cortical surface area,
not by thickness.
So, one can indeed have group-level thickness effects, but if these
aren't accompanied by area effects in the same direction, there may be
no net changes in volume.
Btw, we have just put a paper onbioRxiv
<https://doi.org/10.1101/074666>in which we use NPC to capture these
effects that could remain unseen when volume is analysed alone. In the
same paper we also propose a different method to measure volume in
surface models that is no longer just the product of area by thickness
(this new method is now the default in FreeSurfer 6.0, thanks do Doug
Greve who made it available there).
All the best,
Anderson"
By noise, I just mean variability, which could come from those
sources, but more likely come from intersubject variability. No good
way to check those. It is looking like volume analysis has much higher
false positive rates than thickness too.
On 5/2/17 12:29 PM, John Anderson wrote:
-------- Original Message --------
Subject: Re: Volume vs cortical thickness
Local Time: May 2, 2017 12:29 PM
UTC Time: May 2, 2017 4:29 PM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Thank you Doug,
One more question please.
Noise: does this mean low quality /high quality T1 images regarding
SNR and contrast between white and gray matter.
What is the correct approach to check noise effect on the
reconstructed T1 images to avoid these controversies between cortical
and volumetric measures ?
Thank you for any advice!
You are speaking statistically, I assume? Ie, you see a sig change in
volume and not thickness, or vice versa? If so, it can easily be
explained by differences in noise
On 5/2/17 5:00 AM, John Anderson wrote:
-------- Original Message --------
Subject: Re: Volume vs cortical thickness
Local Time: May 2, 2017 5:00 AM
UTC Time: May 2, 2017 9:00 AM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Hi Doug,
Thank you for the detailed explanation!
Please I have one follow-up question and I highly appreciate your input
How can we explain results related to reduce cortical thickness and
normal gray matter volume. Are these parameters two different thing
or they are related to each other.? In other words:
If (cortical thickness = gray matter volume * area ) that means
reduce cortical thickness must be accompanied by reduce gray matter
volume and vice versa.
My question is: Have you seen similar cases for a reduction in
cortical thickness and normal gray matter volume. I f yes how can
this, at least, be explained mathematically.
All the best,
John
The thickness is an average of two numbers. One is the distance from
a white surface vertex to the pial surface along the normal to the
white. The other is the distance from the pial to the white along
the normal to the pial.
Volume (in v6) is computed as the volume of a truncated tetrahedron.
Prior to v6 it was surface area times thickness
-------- Original Message --------
Subject: Volume vs cortical thickness
Local Time: April 10, 2017 12:24 PM
UTC Time: April 10, 2017 4:24 PM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Dear Freesurfer experts,
I highly appreciate if anybody clarify how Freesurfer calculate
cortical thickness and gray matter volume.
If the cortical thickness of e.g. precentral gurus is measured as
the closest distance from the gray-white boundary to the gray-CSF
boundray at each vertex on the tessellated surface (Fischl and Dale.
2000).
How the gray matter volume for the precentral gyrus was measured?
Thank you for any clarification!
John
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/
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