I'm not sure it matters, but if you put it at the end nothing will reset
it
On Thu, 14 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Yes, that is my end goal. I have a patient i edited the aseg to include
left-cerebral white matter
and also, want to normalize the intensity using expert option. Where should I
place the
"-canorm-usecps" flag ? After the command like " recon-all -autorecon2
-autorecon3 -expert -parallel
-openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like
"recon-all -autorecon2
-canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time.
Thank you.
Best,
Paul
On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl <[email protected]>
wrote:
do you want the control points to be applied to the aseg? If so, you need
to also
specify -canorm-usecps
cheers
Bruce
On Thu, 14 Sep 2017, miracle ozzoude wrote:
Thanks Bruce. Yes, I want to regenerate the aseg and also use the
expert
option for control point.
That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8
-bigventricles -3T time.
Best,
Paul
On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl
<[email protected]>
wrote:
do you want it to regenerate the aseg? If not, then a). If
so, then
you would just run
autorecon2 (instead of autorecon2-cp)
cheers
Bruce
On Thu, 14 Sep 2017, miracle ozzoude wrote:
I used the expert option for control points and
manually edited
the
aseg.presurf.mgz. Which is the
proper flag to use in other to incorporate the
respective
changes?
a) recon-all -autorecon2-cp -autorecon2-noaseg
-autorecon3
-expert -parallel
-openmp 8
-bigventricles -3T -time
or
b) recon-all -autorecon2-cp -autorecon3 -expert
-parallel
-openmp 8
-bigventricles -3T -time
Thanks.
Best,
Paul
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