Hi David
1. I think the main function of the 3T flag is to align to an Talairach
average of 3T data, so probably you should continue to use it.
2. There really is no hard threshold. For the control points you want to
use voxels that are entirely wm , no partial voluming and no pathology.
3. You can change some bounds in mri_segment and mris_make_surfaces that
will make it more/less aggressive. The help in that command contains
some documentation on them. Unfortunately we haven't had the time to
document them more thorougly. We'll try to get to it soon
cheers
Bruce
On Tue, 27 Nov 2018, David S Lee wrote:
External Email - Use Caution
Hello FreeSurfer Experts!
I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans
through recon-all
pipeline. The correction has solved many segmentation errors which reduced the
time spent on manual
editing. I have several questions related to this:
1. I am aware of the "3T" flag that can be supplied to recon-all command. It
seems redundant to use
this flag for already-bias-corrected 3T scans (testing from my end also
confirms this), but do you
recommend any other bias-correction steps?
2. What are the minimum and maximum intensity thresholds set for GM and WM
during recon-all? In the
official control point tutorial, it suggests that WM should be "close" to
intensity of 110, but I
wanted to know the exact thresholds to perform more accurate manual editing.
3. If these GM and WM intensity parameters can be changed from default, do you
recommend doing so?
If there is a documentation I can refer to find answers (I've failed to find
one so far), please let
me know.
Thank you for your time as always,
--
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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