Dear Paul,
mris_expand can be used only in the hypothetical cases, where in all brain
systematically the surface is shifted to equal amount from the position which
is anatomically relevant.
Therefore it cannot be used to correct for local errors. To ilustrate the use
of this tool, see the scre
Hello Antonin,
GM/WM boundary = thickness. correct me if i am wrong. Shouldn't
expanding/shrinking the ?h.white or ?h.pial surface to the correct size and
shape help with that? I have moved the position of the ?h.white to capture
most of the WM using mris_expand but i haven't been successfully with
Dear Paul,
I am quite surprised that you were successful to estimate correct GM/WM
boundary using this tool. As far as I know and looking at the source code, this
tool GLOBALLY moves the position of the specified surface to some amount, so it
cannot be used to correct local errors. It is used e
Thanks bruce for your response. I am trying to expand the pial surface (see
attached image) in order to estimate the GM/WM boundary properly. I have
successfully expanded the white matter but when i tried the mris_expand
scripts for pial surface (mris_expand -thickness lh.pial 0.5 lh.newpial),
the
Hi Paul
it's hard to answer your questions without knowing what you are trying to
achieve
cheers
Bruce
On Wed, 11 Jan 2017, miracle ozzoude wrote:
Hello freesurfer,
I have several questions about mris_expand command. I know it can be used to
expand or shrink a point on a surface by a fixed
Hello freesurfer,
I have several questions about mris_expand command. I know it can be used
to expand or shrink a point on a surface by a fixed amount or distance. My
questions are:
1) Can it be used to expand the pial surface? if yes, please can you
confirm if this is the right script= mris_expan
Hi Alex
if you upload the subject that is causing this problem I'll take a look.
What version are you running and what OS?
cheers
Bruce
On Thu, 22 Oct 2015, Alex Puckett
wrote:
Hello!
I'm having trouble with mris_expand using the -thickness flag. If I expand
by a fixed distance instead
Hello!
I'm having trouble with mris_expand using the -thickness flag. ?If I expand by
a fixed distance instead of % thickness then mris_expand works no problem -
the program seems to be hanging up when reading the thickness file. Has anyone
else experienced this?
The command I'm running (fr
.
- Andrew
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 23, 2012 9:44 AM
To: Andrew C Yourich
Cc: freesurfer@nmr.mgh.harvard.edu; Robert C Knowlton;
gramf...@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mris_expand not working since
.harvard.edu]
> Sent: Sunday, April 22, 2012 9:10 AM
> To: Andrew C Yourich
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0
>
> Hi Andrew,
>
> I just tried this and it worked fine for me. If you tell me
il to
Alex and then view it in freeview to see if anything has changed.
Thanks,
Andrew
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Sunday, April 22, 2012 9:10 AM
To: Andrew C Yourich
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
Hi Andrew,
I just tried this and it worked fine for me. If you tell me what
os/hardware you are running on I'll send you a current binary and you can
see if that works.
cheers
Bruce
p.s. do you look at the surfaces via:
freeview -f lh.white lh.white.expanded
On Fri, 20 Apr 2012, Andrew C
Hello,
I have recently upgraded from running version 4.0.2 of Freesurfer to the most
current version (v.5.1.0), and have encountered a problem. I used to be able to
expand the recon-all generated white matter volume by a percentage of the grey
matter thickness using mris_expand, but ever sinc
Hi Reza,
what version are you running, and what is your command line? In the current
version, this works for me:
mris_expand -n 11 -thickness \
/homes/4/fischl/local_subjects/bruce/surf/lh.white 1 \
/homes/4/fischl/local_subjects/bruce/surf/lh.mid \
this will create surfaces nam
Hello,
I've tried running mris_expand on several different surfaces, with or
without the -thickness flag, and while it ends without error and creates
the output file, the output looks identical to the input. I've tried even
expanding by large amounts, large percentages of thickness values, but
wit
how about the thickness files? Is there space left on the disk?On Fri, 19
Feb 2010, Gregory Dierksen wrote:
>
> Yes, I can view both the left and right white matter surfaces in tksurfer.
>
> Sorry for the delay, and thanks for your help.
>
> Greg
>
> On Thu, 18 Feb 2010, Douglas N Greve wrote:
>
That should work, but I would recommend using
recon-all -s subject -finalsurfs
you can spec a hemi if it is only the rh
doug
Gregory Dierksen wrote:
>
> Ok, there's the problem. rh.thickness will not load as an overlay and
> returns the Input/Output error message.
>
> So can I just run the co
Ok, there's the problem. rh.thickness will not load as an overlay and
returns the Input/Output error message.
So can I just run the command
mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs rh
to re-generate the right hemisphere thickness file?
On Fri, 19 Feb 2010, Douglas N Greve wrote
Sorry, it looks like it is the thickness file, not the white surface, it
is having problems with. Can you load the thickness as an overlay?
Gregory Dierksen wrote:
>
> Yes, I can view both the left and right white matter surfaces in
> tksurfer.
>
> Sorry for the delay, and thanks for your help.
Yes, I can view both the left and right white matter surfaces in tksurfer.
Sorry for the delay, and thanks for your help.
Greg
On Thu, 18 Feb 2010, Douglas N Greve wrote:
> An Input/Output error often means that the disk is corrupted or possibly
> full. Can you read the the lh.white with some
An Input/Output error often means that the disk is corrupted or possibly
full. Can you read the the lh.white with something else? Eg, can you
load it with tksurfer?
doug
Gregory Dierksen wrote:
> Hi,
>
> I'm trying to make a "midgray" surface by inflating the white surface of a
> subject by 5%
Hi,
I'm trying to make a "midgray" surface by inflating the white surface of a
subject by 5% using the following command:
mris_expand -thickness rh.white 0.5 rh.midgray.05
I am getting the following output:
using distance as a & of thickness
expanding surface rh.white by 0.50% of thickness an
oops, you're right. -t does something else that is irrelevant. There is
code around for supersampling the surface, but it's not integrated into
anything yet. I assume you have the source so you should be able to try it
out if you want.
cheers,
Bruce
On Tue, 6 Oct 2009, Don Hagler wrote:
>
>
Bruce recently wrote that you could run mris_expand like this:
mris_expand -t lh.white 0.5 lh.graymid
I found that didn't work, but this did:
mris_expand -thickness lh.white 0.5 lh.graymid
I am using version 4.4.
By the way, is there a way to increase the resolution of the surfaces before
cre
dev mris_expand found at:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/linux-centos4_x86_64/
On Fri, 2009-07-24 at 14:53 +0200, Lars Tjelta Westlye wrote:
> Here you go:
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0
>
> RedHat release: Red Hat Enterprise Linu
Here you go:
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0
RedHat release: Red Hat Enterprise Linux Client release 5.3 (Tikanga)
Kernel info: Linux 2.6.18-128.1.6.el5 x86_64
Thanks a lot!
> Hi Lars,
>
> I recently fixed mris_expand to take negative distances. If you send us
Hi Lars,
I recently fixed mris_expand to take negative distances. If you send us
your hardware/software platform we'll send you a dev version
Bruce
On Fri, 24 Jul 2009, Lars Tjelta Westlye wrote:
> Perfect, thanks. I'm also trying to display a surface at a fixed distance
> into the WM relative
Perfect, thanks. I'm also trying to display a surface at a fixed distance
into the WM relative to the white surface.
mris_expand lh.white -1 lh.wm1mm
does not seem to do what I want. Is what I'm trying to do feasible with
mris_expand or would you suggest another tool?
> Hi Lars,
>
> that is wha
Hi Lars,
that is what it does by default, unless you give it the -thickness flag.
cheers,
Bruce
On
Fri, 24 Jul 2009, Lars Tjelta Westlye wrote:
> Hi,
>
> how can I tell mris_expand to expand the surface by a fixed distance
> rather than by a fraction of the thickness?
>
> Thanks,
> Lars
>
> ___
Hi,
how can I tell mris_expand to expand the surface by a fixed distance
rather than by a fraction of the thickness?
Thanks,
Lars
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
30 matches
Mail list logo
