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 on [bioRxiv](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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