Thanks bruce, like creating expert.opts text file in the scripts directory and inserting
the command "mri_normalize -norm-b 25". Right? This is the modified script
1 #!bin/bash -eux
2 set -e
3 echo -e "EntireFreeSurferpipelinewithAutocontrolpoints"
4
5 SubjectID="$1"
6 SubjectDIR="$2"
7 T1="$3" #T1 FreeSurfer Input
8 T2="$4" #T2 FreeSurfer Input
9
10 recon-all -autorecon-all -i $T1 $T2 T2pial -s $SubjectID -parallel -hires
11 #we need to get aseg, brainmask, norm, brain
12 aseg=$SubjectDIR/$SubjectID/mri/aseg.presurf.mgz
13 brainmask=$SubjectDIR/$SubjectID/mri/brainmask.mgz
14 norm=$SubjectDIR/$SubjectID/mri/norm.mgz
15 brain=$SubjectDIR/$SubjectID/mri/brain.mgz
16
17 #make sure to create an expert.opts text file in the SubjectID/scriptsdirectory
like this (SubjectID/scripts/expert.opts) and write down the command line
"mri_normalize -norm2-b 25
18 echo "mri_normalize -norm2-b 25" > x.opts
19
20 #include T2pial since you are rerun -autorecon3
21 recon-all -s $SubjectID -autorecon2-cp -autorecon3 -expert x.opts
22
23 echo -e "done"
2) Since I am rerun -autorecon2-cp and -autorecon3 then, do I need the T2pial
flag.
3) I named the expert option file expert.opts, shouldn't I replace the
"x.opts" with the name of the file (please see lines 18 and 21)
4) For line 18, any reason why you suggested I remove "mri_normalize -mprage
-norm2-b 25 -aseg $aseg -mask $brainmask $norm $brain"?
5) Do I need to specify the path to the expert.opts files?
Cheers,
Pascal
On Mon, Feb 6, 2017 at 9:42 AM, Bruce Fischl <[email protected]> wrote:
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
<[email protected]> 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
<[email protected]> 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
<[email protected]> 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
<[email protected]>
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
<[email protected]>
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
<[email protected]>
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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