Thanks Bruce. Please can you confirm if this script is
correctSubjectID="$1"SubjectDIR="$2"
T1="$3" #T1 FreeSurfer Input
T2="$4" #T2 FreeSurfer Input
recon-all -autorecon-all -i $T1 $T2 T2pial -s $SubjectID -parallel -hires
# we need to get aseg, brainmask, norm, brain
aseg=$SubjectDIR/$SubjectID/mri/aseg.presurf.mgz
brainmask=$SubjectDIR/$SubjectID/mri/brainmask.mgz
norm=$SubjectDIR/$SubjectID/mri/norm.mgz
brain=$SubjectDIR/$SubjectID/mri/brain.mgz
echo "mri_normalize -mprage -norm2-b 20 -aseg $aseg -mask $brainmask $norm $brain"
> x.opts
recon-all -s $SubjectID -autorecon2-cp -autorecon3 -expert x.opts
echo "done"
Also, do i need to include T2pial in -autorecon2-cp?
Cheers,
Pascal
On Fri, Feb 3, 2017 at 3:53 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
no, more like:
echo "mri_normalize -b 20" > x.opts
recon-all -s subjectID -autorecon2-cp -autorecon3 -expert x.opts
or if you ware starting from scratch, use your command with the -expert
x.opts
stuff at the end
cheers
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
<fis...@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
<fis...@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
<fis...@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
<fis...@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
<fis...@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
<fis...@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
_______________________________________________
Freesurfer mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
information in
this e-mail
is intended
only for the
person to
whom it is
addressed. If you
believe this
e-mail was
sent to you in
error and
the e-mail
contains patient
information,
please contact
the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If
the e-mail
was sent to
you in error
but
does not contain
patient
information,
please contact
the sender
and properly
dispose
of the
e-mail.
_______________________________________________
Freesurfer mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in
this e-mail
is intended
only for the
person to
whom it is
addressed. If you
believe this
e-mail was
sent to you in
error and
the e-mail
contains patient
information,
please contact
the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If
the e-mail
was sent to
you in error
but does not
contain patient
information,
please contact
the sender
and properly
dispose of the
e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail
is intended
only for the
person to
whom it is
addressed. If you believe this
e-mail was
sent to you in
error and
the e-mail
contains patient information,
please contact
the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If
the e-mail
was sent to
you in error
but does not contain patient
information,
please contact
the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended
only for the
person to
whom it is
addressed. If you believe this e-mail was
sent to you in
error and
the e-mail
contains patient information, please
contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If
the e-mail
was sent to
you in error
but does not contain patient information,
please contact
the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to
whom it is
addressed. If you believe this e-mail was sent to you
in error and
the e-mail
contains patient information, please contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail
was sent to
you in error
but does not contain patient information, please
contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
