Hi Paul
it's to help with cortex where the deep layers are heavily myelinated and the gray/white boundary isn't as big a jump in contrast as infragranular/supragranular. It usually is only needed for hires data
cheers
Bruce
On Mon, 9 Jan 2017, miracle ozzoude wrote:
hello Bruce, I have another question, what's the function of -first_wm_peak
in mris_make_surfaces? I know it helps "settle WM surface at first peak in
intensity profile insted of highest". what does this mean and do I need to
specify a value for it. Thanks.
Best,
Paul
On Mon, Jan 9, 2017 at 4:19 PM, miracle ozzoude <miracooloz@gmail.com>
wrote:
Thanks a lot Antonin.I will try it out. I am trying to figure
out how to use mris_make_surfaces to extend my pial surface with
T2 argument included and also, play around with -first_wm_peak
and -nsigmas
On Mon, Jan 9, 2017 at 4:06 PM, Antonin Skoch <ansk@ikem.cz> wrote:
Dear Paul,
you can also try to play with "reposition surface" tool in freeview, where y
ou (apart from other options) can directly edit coordinates of the surface v
ertices.
However, this tool is not well documented and I myself would like to know th
e significance of some of the parameters - see my unanswered post from 4th j
anuary 2017:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ msg50759.html
And, I am not sure how this works in 5.3 version of freeview, I have used it
only in V6beta (dev) version.
Regards,
Antonin
I think this problem is fixed in 6.0 (if and when we get it out)
On Mon, 9 Jan 2017, miracle ozzoude wrote:
Thanks bruce for your response. I accidentally listed number 3 twice instead
of 4. Here's my 4th question: Which of the mris_make_surfaces can I use to
correct the pial surface when it does cross the white matter and also, which
is helpful with white matter surface extension? Please see attached
screenshot. I came across a post with similar error in the forum and you
diagnosed but it wasn'tfix
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-A pril/045097
.html
Best,
Paul
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