Hi Pascal
I think you need to put it in an xopts file as the command line calls -mprage after -b 20 and so will reset it. BTW: I used all the way up to -b 25 and things improved, so you might try that. At some point you will start eroding the gray/white boundary as you increase the -b threshold, but 25 looked ok to me
Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Thanks bruce. That's
Line 1 recon-all -all -i T2 T2pial -s subjectID -parallel
Line 2 mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
This is in visual studio code
Cheers,
Pascal
On Fri, Feb 3, 2017 at 3:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Pascal
you can put the
mri_normalize -b 20
line in a file, and use it as the expert options in recon-all to rerun autorecon2-cp and
autorecon3 with it
cheers
Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Thanks bruce. After running mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz
-mask brainmask.mgz
norm.mgz brain.mgz, do I need to run recon-all -autorecon2 -autorecon3
again? Cheer.,
Pascal
On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Pascal
yes, that is the right command line. I don't know if you will need more
control points, but
that helped a lot. -a specifies the intensity threshold above 110 and -g
specifies the
spatial gradient for the 1d normalization
cheers
Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Hello Bruce, Thank you very much.
a) The mri_normalization command line is where control points starts
(normalization2). Right?
b) Also, is this right command " mri_normalize -mprage -b 20 -aseg
aseg.presurf.mgz -mask brainmask.mgz
norm.mgz brain.mgz"?
c) Do I need any other flag besides -b?
d) I don't need to make the manual control point edits right?
e) Lastly, what does -a (float a) and -g (float g) mean?
Cheers,
Pascal
On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
HI Pascal
I got significantly improved results using -b 20 on the
mri_normalize
command line. Note
that this has to come after the mprage. I think you can do it
with an
expert options file
with:
mri_normalize -b 20
cheers
Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Hello Bruce, I sent it.
Pascal
On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
tar and gzip an example subject directory and send
us the
voxel coords of
points you want us
to look at
cheers
Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Thanks bruce. Do I upload the entire file?
Also,where
can I find the
link? Pascal
On Fri, Feb 3, 2017 at 10:35 AM, Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Pascal
I don't think tissue priors will help
due to the
complexity
and
variability of the folding
patterns. There may be other
interventions though
- can you
send us some
examples of where
things don't look accurate to you?
cheers
Bruce
On Fri, 3 Feb 2017, Pascal Goodman
wrote:
Hello Bruce, Thanks for
replying. I am
trying find ways
to improve
white matter
surface (to reduce
manual intervention by control
points) with
the
probability map.
Also, how do I
extract the multiple
prior maps you mentioned. Thank
you.
Best,
Pascal
On Fri, Feb 3, 2017 at 10:22 AM,
Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Pascal
what are you trying to
achieve?
Internally we have
multiple
prior maps of
this type, but I
don't think we are setup
for a user to
supply a
different one
cheers
Bruce
On Fri, 3 Feb 2017, Pascal
Goodman
wrote:
Hello Freesurfer, I
do have a
question. Can
FS take
probability maps
of tissue
segmentation as
prior?
Thanks,
Pascal
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