Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't run it with -n. Without it, it will run until it asymptotes. I would try:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user could access it outside of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere in 160 iterations, writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output patch>
I'm not certain if <output patch> is synonymous with output surface? Also, what is the purpose of a <patch file name>? Thanks.
Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fischl@nmr.mgh.harvard.edu To: xuelongzhao@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, many of our binaries take the -w <n> flag to write out a snapshot of the minimization every nth step, including mris_sphere
cheers Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
Is it also possible to track the inflation all the way to the sphere? I was hoping
that
I could take snapshots of equi-area intermediate forms as the cortex is unfolded
onto
the sphere instead of stopping at the inflated cortex. Thanks.
Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
you can use -w 1 to write out every step in the inflation process and choose what you want. If you want it to preserve surface area during inflation (as opposed to just at the end), also include -scale 1
cheers Bruce
On Wed, 9 Apr 2014, Xuelong Zhao wrote:
Hi,
I would like to ask whether it is possible to display different levels of cortical inflation?
I have been using the command: mris_inflate
but the -dist and -n flags do not seem to make that much difference. Also, if I use fsaverage lh.orig as the input file and using the default options for mris_Inflate I don't seem to be able to recover the lh.inflated surface.
Are there any alternative commands to control the level of inflation? Thanks.
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
yes, that would help On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't run it with -n. Without it, it will run until it asymptotes. I would try:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user could access it
outside
of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere in 160
iterations,
writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output patch>
I'm not certain if <output patch> is synonymous with output surface? Also, what is
the
purpose of a <patch file name>? Thanks.
Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fischl@nmr.mgh.harvard.edu To: xuelongzhao@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, many of our binaries take the -w <n> flag to write out a snapshot of the minimization every nth step, including mris_sphere
cheers Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
Is it also possible to track the inflation all the way to the sphere? I was
hoping
that
I could take snapshots of equi-area intermediate forms as the cortex is
unfolded
onto
the sphere instead of stopping at the inflated cortex. Thanks.
Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
you can use -w 1 to write out every step in the inflation process and choose what you want. If you want it to preserve surface area during inflation (as opposed to just at the end), also include -scale 1
cheers Bruce
On Wed, 9 Apr 2014, Xuelong Zhao wrote:
> Hi, > > I would like to ask whether it is possible to display different levels of > cortical inflation? > > I have been using the command: mris_inflate > > but the -dist and -n flags do not seem to make that much difference. Also, > if I use fsaverage lh.orig as the input file and using the default options > for mris_Inflate I don't seem to be able to recover the lh.inflated
surface.
> > Are there any alternative commands to control the level of inflation? > Thanks. > > > > _______________________________________________ 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
I attempted the run again using
mris_sphere -w 1 -scale 1 lh.inflated lh.sphere_test
However, even with the -w 1 set the intermediate surfaces are all very close to the sphere. Are there any other flags I could try?
Date: Fri, 11 Apr 2014 10:25:56 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, that would help On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't run it with -n. Without it, it will run until it asymptotes. I would try:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user could access it
outside
of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere in 160
iterations,
writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output patch>
I'm not certain if <output patch> is synonymous with output surface? Also, what is
the
purpose of a <patch file name>? Thanks.
Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fischl@nmr.mgh.harvard.edu To: xuelongzhao@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, many of our binaries take the -w <n> flag to write out a snapshot of the minimization every nth step, including mris_sphere
cheers Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
Is it also possible to track the inflation all the way to the sphere? I was
hoping
that
I could take snapshots of equi-area intermediate forms as the cortex is
unfolded
onto
the sphere instead of stopping at the inflated cortex. Thanks.
Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
you can use -w 1 to write out every step in the inflation process and choose what you want. If you want it to preserve surface area during inflation (as opposed to just at the end), also include -scale 1
cheers Bruce
On Wed, 9 Apr 2014, Xuelong Zhao wrote:
> Hi, > > I would like to ask whether it is possible to display different levels of > cortical inflation? > > I have been using the command: mris_inflate > > but the -dist and -n flags do not seem to make that much difference. Also, > if I use fsaverage lh.orig as the input file and using the default options > for mris_Inflate I don't seem to be able to recover the lh.inflated
surface.
> > Are there any alternative commands to control the level of inflation? > Thanks. > > > > _______________________________________________ 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
_______________________________________________ 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.
if it's just for visualization you ca use -i, but in general we just project and unfold on the sphere (and don't use -i which inflates and drives the surface to the sphere)
On Sat, 12 Apr 2014, Xuelong Zhao wrote:
I attempted the run again using
mris_sphere -w 1 -scale 1 lh.inflated lh.sphere_test
However, even with the -w 1 set the intermediate surfaces are all very close to the sphere. Are there any other flags I could try?
Date: Fri, 11 Apr 2014 10:25:56 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, that would help On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh
.orig as the
input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of them
were nearly
spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even
so, it seems
its very hard to capture the unfolding process from the cortex to the sphe
re. Should I
be using some other flags? For instance, if I used -w 1 instead, would thi
s help?
Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags. Is i
t also
possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn'
t
run it with -n. Without it, it will run until it asymptotes. I would try
:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user could a
ccess it
outside
of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to b
e complete. I
used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere in
160
iterations,
writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output patch>
I'm not certain if <output patch> is synonymous with output surface? A
lso, what is
the
purpose of a <patch file name>? Thanks.
Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fischl@nmr.mgh.harvard.edu To: xuelongzhao@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, many of our binaries take the -w <n> flag to write out a snapsh
ot of
the minimization every nth step, including mris_sphere
cheers Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
Is it also possible to track the inflation all the way to the sphe
re? I was
hoping
that
I could take snapshots of equi-area intermediate forms as the cort
ex is
unfolded
onto
the sphere instead of stopping at the inflated cortex. Thanks.
> Date: Wed, 9 Apr 2014 08:31:46 -0400 > From: fischl@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > CC: greve@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Intermediate stages of cortical inflat
ion
> > you can use -w 1 to write out every step in the inflation proces
s and
> choose what you want. If you want it to preserve surface area du
ring
> inflation (as opposed to just at the end), also include -scale 1 > > cheers > Bruce > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > Hi, > > > > I would like to ask whether it is possible to display differen
t levels of
> > cortical inflation? > > > > I have been using the command: mris_inflate > > > > but the -dist and -n flags do not seem to make that much diffe
rence. Also,
> > if I use fsaverage lh.orig as the input file and using the def
ault options
> > for mris_Inflate I don't seem to be able to recover the lh.inf
lated
surface.
> > > > Are there any alternative commands to control the level of inf
lation?
> > Thanks. > > > > > > > > > _______________________________________________ > 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 t
o whom it is
> addressed. If you believe this e-mail was sent to you in error a
nd the e-mail
> contains patient information, please contact the Partners Compli
ance 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 sen
der and
properly
> dispose of the e-mail. >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.
Great, the -i option is exactly what i needed. Just to clarify, does this use the same algorithm as mris_inflate?
Also, I tried using mris_sphere with the -i and -scale 1 flags, but it doesn't seem area was preserved when I viewed in Freeview. Is there a way to also enforce the surface area? Thanks.
Date: Sat, 12 Apr 2014 00:53:34 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
if it's just for visualization you ca use -i, but in general we just project and unfold on the sphere (and don't use -i which inflates and drives the surface to the sphere)
On Sat, 12 Apr 2014, Xuelong Zhao wrote:
I attempted the run again using
mris_sphere -w 1 -scale 1 lh.inflated lh.sphere_test
However, even with the -w 1 set the intermediate surfaces are all very close to the sphere. Are there any other flags I could try?
Date: Fri, 11 Apr 2014 10:25:56 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, that would help On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh
.orig as the
input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of them
were nearly
spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even
so, it seems
its very hard to capture the unfolding process from the cortex to the sphe
re. Should I
be using some other flags? For instance, if I used -w 1 instead, would thi
s help?
Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags. Is i
t also
possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn'
t
run it with -n. Without it, it will run until it asymptotes. I would try
:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user could a
ccess it
outside
of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to b
e complete. I
used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere in
160
iterations,
writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output patch>
I'm not certain if <output patch> is synonymous with output surface? A
lso, what is
the
purpose of a <patch file name>? Thanks.
Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fischl@nmr.mgh.harvard.edu To: xuelongzhao@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, many of our binaries take the -w <n> flag to write out a snapsh
ot of
the minimization every nth step, including mris_sphere
cheers Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
> Is it also possible to track the inflation all the way to the sphe
re? I was
hoping
that
> I could take snapshots of equi-area intermediate forms as the cort
ex is
unfolded
onto
> the sphere instead of stopping at the inflated cortex. Thanks. > > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400 > > From: fischl@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > CC: greve@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflat
ion
> > > > you can use -w 1 to write out every step in the inflation proces
s and
> > choose what you want. If you want it to preserve surface area du
ring
> > inflation (as opposed to just at the end), also include -scale 1 > > > > cheers > > Bruce > > > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > > > Hi, > > > > > > I would like to ask whether it is possible to display differen
t levels of
> > > cortical inflation? > > > > > > I have been using the command: mris_inflate > > > > > > but the -dist and -n flags do not seem to make that much diffe
rence. Also,
> > > if I use fsaverage lh.orig as the input file and using the def
ault options
> > > for mris_Inflate I don't seem to be able to recover the lh.inf
lated
surface.
> > > > > > Are there any alternative commands to control the level of inf
lation?
> > > Thanks. > > > > > > > > > > > > > > _______________________________________________ > > 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 t
o whom it is
> > addressed. If you believe this e-mail was sent to you in error a
nd the e-mail
> > contains patient information, please contact the Partners Compli
ance 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 sen
der and
properly
> > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.
yes, it's pretty much the same algorithm, and no you cannot preserve surface area as we are essentially mapping to the unit sphere (actually it's a sphere with r=100mm I think, but there is really no difference)
cheers Bruce
On Mon, 14 Apr 2014, Xuelong Zhao wrote:
Great, the -i option is exactly what i needed. Just to clarify, does this use the same algorithm as mris_inflate?
Also, I tried using mris_sphere with the -i and -scale 1 flags, but it doesn't seem area was preserved when I viewed in Freeview. Is there a way to also enforce the surface area? Thanks.
Date: Sat, 12 Apr 2014 00:53:34 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
if it's just for visualization you ca use -i, but in general we just project and unfold on the sphere (and don't use -i which inflates and drives the surface to the sphere)
On Sat, 12 Apr 2014, Xuelong Zhao wrote:
I attempted the run again using
mris_sphere -w 1 -scale 1 lh.inflated lh.sphere_test
However, even with the -w 1 set the intermediate surfaces are all very
close
to the sphere. Are there any other flags I could try?
Date: Fri, 11 Apr 2014 10:25:56 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
yes, that would help On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and
used lh
.orig as the
input surface):
mris_sphere -w 10 lh.orig lh.sphere_test
However, when I viewed the output of the intermediate forms, all of
them
were nearly
spherical, only lh.sphere_test0010 deviated slightly from the sphere.
Even
so, it seems
its very hard to capture the unfolding process from the cortex to the
sphe
re. Should I
be using some other flags? For instance, if I used -w 1 instead, would
thi
s help?
Thanks.
From: andrewzhao@live.com.au To: fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000
Great, will give this a try. Thanks for clarifying the command flags.
Is i
t also
possible to specify the scale using the flag - scale 1?
Date: Fri, 11 Apr 2014 01:38:01 -0400 From: fischl@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
sorry, it shouldn't say "patch", but "file". We will fix that. I
wouldn'
t
run it with -n. Without it, it will run until it asymptotes. I would
try
:
mris_sphere -w 20 lh.inflated lh.sphere
cheers Bruce
cheers Bruce
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Thanks for pointing this binary out- I didn't realize the user
could a
ccess it
outside
of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem
to b
e complete. I
used it in the following format but not sure if this is correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
I want to check that the above command converts lh.org to a sphere
in
160
iterations,
writes out every 20th iteration and ensures the area is preserved?
Also, on the fswiki site:
mris_sphere [options] <surface file> <patch file name> <output
patch>
I'm not certain if <output patch> is synonymous with output
surface? A
lso, what is
the
purpose of a <patch file name>? Thanks.
> Date: Thu, 10 Apr 2014 11:30:15 -0400 > From: fischl@nmr.mgh.harvard.edu > To: xuelongzhao@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Intermediate stages of cortical
inflation
> > yes, many of our binaries take the -w <n> flag to write out a
snapsh
ot of
> the minimization every nth step, including mris_sphere > > cheers > Bruce > > > On Thu, 10 Apr 2014, Xuelong Zhao wrote: > > > Is it also possible to track the inflation all the way to the
sphe
re? I was
hoping
that > > I could take snapshots of equi-area intermediate forms as the
cort
ex is
unfolded
onto > > the sphere instead of stopping at the inflated cortex. Thanks. > > > > > > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400 > > > From: fischl@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > CC: greve@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Intermediate stages of cortical
inflat
ion
> > > > > > you can use -w 1 to write out every step in the inflation
proces
s and
> > > choose what you want. If you want it to preserve surface
area du
ring
> > > inflation (as opposed to just at the end), also include
-scale 1
> > > > > > cheers > > > Bruce > > > > > > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > > > > > Hi, > > > > > > > > I would like to ask whether it is possible to display
differen
t levels of
> > > > cortical inflation? > > > > > > > > I have been using the command: mris_inflate > > > > > > > > but the -dist and -n flags do not seem to make that much
diffe
rence. Also,
> > > > if I use fsaverage lh.orig as the input file and using the
def
ault options
> > > > for mris_Inflate I don't seem to be able to recover the
lh.inf
lated
surface.
> > > > > > > > Are there any alternative commands to control the level of
inf
lation?
> > > > Thanks. > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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 t
o whom it is
> > > addressed. If you believe this e-mail was sent to you in
error a
nd the e-mail
> > > contains patient information, please contact the Partners
Compli
ance 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
sen
der and
properly
> > > dispose of the e-mail. > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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
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and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Xuelong Zhao