Hi Christian,
Thanks! My data quality is generally not very good - this i why i'm changing
the parameters before starting manual editing (this saves me a lot of work). I
just wanted to make sure that it did not affect the atlas more than necessary
-> making the data incomparable.
Lets have a talk at DRCMR - i also have some questions concerning movement
artefacts.
Best, Silas
Date: Mon, 16 Feb 2015 15:28:46 +0100
From: ct...@dtu.dk
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas -
consequences?
Hi Silas,
Changing the wsthresh and wsgatlas parameters only affect the
brainmask (which is, among other things, used to limit how far the
pial surface is allowed to grow). This shouldn't affect the white
matter.
if your data contrast is good, you generally wont see much affect
from adjusting these parameters. However, if the contrast is bad you
need to inspect your brainmasks carefully, to make sure they
improved (without removing actual brain from the image).
Furthermore, in this case it is likely you'll also need to edit the
brainmasks manually.
To answer your question: Whenever you modify the parameters, and in
particular if you need to edit brainmasks, you introduce a bias in
your study (your qualitative evaluation of how good the brainmasks /
pial surfaces are).
You need to consider if adjusting brainmasks is better than letting
the pipeline do its job - which boils down to the number of subjects
you have. The more you have, the more robust your statistics will
be, and the more likely it is that you can leave everything as it
is. However, If you have few subjects, bad data quality (and in
turn, brainmask quality) can really impact your pial surface, and
then it may be best to adjust the masks.
We can talk more at the hospital if you need further discussion, and
also look at your data ;-)
Best,
Christian
On 02/16/2015 01:54 PM, Silas wrote:
Hi Freesurfer team,
I'm currently making an structural analysis using
freesurfer. In the analysis i'm comparing 3 groups; 2 patient
groups with different reactions to a certain type of
medication and a healthy control group. In the freesurfer
pipeline i'm changing the parameters wsthresh and wsgatlas in
order to obtain a better fitted pial surface and white matter
surface - and i was wondering if changing these parameters
affect the comparability of the 3 groups (if e.g. i would like
to investigate the inferior frontal gyrus)?
Best, Silas
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