Hi,
Is it possible to view control points (in control.dat), that you already
created? If so, how do you do it?
Thanks,
Matt.
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Hi Bruce,
That didn't happen, but perhaps because I loaded the volume with -f instead
of the more standard way. I'll try it again.
Thanks,
Matt.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, October 27, 2011 12:53 PM
To: Matt
Hi Michael,
It might have something to do with low myelin content there in general (will
make grey matter harder to tell from CSF) and late myelination (at least
part of the anterior temporal cortex has its white matter myelinate quite
late in development), which would reduce grey/white contrast.
Hi,
I am wondering what tools FreeSurfer has to convert between different affine
matrix formats.
For example, if I had a talairach.xfm that did a better job than
talairach.lta, is there a way to convert from one to the other? What about
FSL FLIRT matricies? Can these be interconverted wit
specific case.
doug
Matt Glasser wrote:
>
> Hi,
>
>
>
> I am wondering what tools FreeSurfer has to convert between different
> affine matrix formats.
>
>
>
> For example, if I had a talairach.xfm that did a better job than
> talairach.lta, is there a
I think Bruce meant:
"the ?h.sulc is the integrated dot
product of the movement vector with the surface normal during inflation."
Peace,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent:
Greg,
I assume you are using the same surfaces as those that I gave you, right?
Thanks,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greg Burgess
Sent: Thursday, March 08, 2012 2:28 PM
To: Douglas N Gr
I'm dredging this 2 year old post up for the benefit of Google and anyone
else who wonders about the cause of this. It is a non-fatal error (for
FreeSurfer, but perhaps not other things) that is caused by having set the
variable:
POSIXLY_CORRECT=1
It causes bc (on Debian/Ubuntu) systems to fail
Hi Greg,
I would say there are a variety of possible confounds for cortical thickness
(e.g. changes in cortical myelin content, changes in the closeness of
opposition between grey matter and the dura from brain atrophy), but that
wouldn't be one of the ones I would think of. White matter hyperint
Is there a way to adjust the grey and white matter of the aseg automatically
based on the surfaces?
Thanks,
Matt.
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The inform
I'd be interested to hear how this goes too.
Thanks,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, May 14, 2012 4:09 PM
To: Joshua Lee
Cc: FreeSurfer
Subject: Re: [Freesurfer]
but no one has
used it yet but me I don't think (unless Matt Glasser has gotten his
version working, which on second thought he probably has)
On Mon, 14
May 2012, Michael Waskom wrote:
> Hi Bruce,
> Is there a flag for this on recon-all? Or do you need to use
> mri_make_surfaces d
$*`
Line. Then one gets the best of both worlds.
Peace,
Matt.
-Original Message-----
From: Matt Glasser [mailto:m...@ma-tea.com]
Sent: Thursday, March 22, 2012 5:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Rather one unsets it like this:
unset POSIXLY_CORRECT
Peace,
Matt.
-Original Message-
From: Matt Glasser [mailto:m...@ma-tea.com]
Sent: Friday, May 18, 2012 12:47 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE
MRICron's dcm2nii does a good job with par and rec files.
Peace,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, August 12, 2009 5:28 PM
To: Lindsay Nagamatsu
Cc: freesurfe
I am curious about how to use mri_convert to convert wmparc.mgz back to the
space that the original nii.gz volume that I gave FreeSurfer was in without
resampling for further analysis with FSL. The volume I imported was
176x208x176, and oriented xorient: Left to Right, yorient: Posterior to
Anteri
Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Sunday, August 23, 2009 5:47 PM
To: Matt Glasser
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space
without Resampling
Hi Matt,
you can give a -rl switch to "reslice like" a templa
wmparc.mgz to Original Volume Space
without Resampling
It depends on the resolution.
On Aug 23, 2009, at 6:53 PM, "Matt Glasser" wrote:
> Hi Bruce,
>
> Presumably all that was done to the volume when it was imported was
> that
> some zero padding around the sides was add
Just do it before you try to run any of the FreeSurfer programs. What
issues are you having? I have FreeSurfer installed on a number of Ubuntu
machines.
Peace,
Matt.
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ah
I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar
Sent: Monday, August 24, 2009 10:04 AM
To: Ahmed, F, Me
Cc: Freesurfer Mai
mri_convert, I want to specifically return to the same 111 volume size
and space and I provided as accurately as possible (hopefully using
the inverse of the total transform applied to the image during
processing). I know Matt Glasser has worked out a way to convert (and
apparently re-register
That looks correct to me.
Peace,
Matt.
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Mehul Sampat
Sent: Thursday, November 05, 2009 3:38 PM
To: Freesurfer Mailing List
Subject: [Freesurfer] reslicing question
Hi
I am wondering if it is necessary to perform the taltransform (or care about
the results when it fails) to get good surfaces of non-human primate brains?
I know I can go in and manually edit it to get it right, but I would rather
not do this if it isn't critical for surface generation. Is it okay
PM
To: Matt Glasser
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach on Non-human Primates
Hi Matt,
it shouldn't be needed for non-human primates, and in fact will probably
mess things up. I thought the -monkey switch disabled it, but I could be
wrong.
cheers
Bruce
O
nkeys.
Peace,
Matt.
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Friday, December 25, 2009 10:20 AM
To: Bruce Fischl
Cc: Matt Glasser; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach on Non-human Primates
i'm not familiar with
Hi,
I am wondering if there is a way to apply the default surface based
registration that is done during recon-all to surfaces other than the sphere
so that the nodes are all lined up? I am wanting to have registered white
matter surfaces that I can map data from the volume to the surface to a
eg is registered across
subjects, it is sufficient to register the wm surfaces.
doug
Matt Glasser wrote:
>
> Hi,
>
>
>
> I am wondering if there is a way to apply the default surface based
> registration that is done during recon-all to surfaces other than the
> sphere so
er res). Bruce might have more insight.
>
> doug
>
> Matt Glasser wrote:
>> Hi Doug,
>>
>> Thanks for your response. How does one go about getting registered white
>> matter surfaces then? I would like all of the surfaces to be registered
so
>> that they have the s
sities),
rather than the surfaces themselves. I think you need the surfaces for
your tractography stuff.
But if all you need is average metric data on average40, then I doubt
you need the individual surfaces on a standard mesh.
Donna
On 03/02/2010 12:58 PM, Matt Glasser wrote:
> Hi Dou
It is possible to do this sort of thing in Caret (using the FreeSurfer
registration); one can create a deformation map between sphere and
sphere.reg. What do you need the deformation map for?
Peace,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-
I have /usr/lib64/libtiff.so.3 linked to /usr/lib64/libtiff.so.4 which is
linked to /usr/lib64/libtiff.so.4.3.2 in my Lucid 64bit install. See if
libtiff.so.4.3.2 exists on your system in /usr/lib64 and if so:
sudo ln -s /usr/lib64/libtiff.so.4.3.2 /usr/lib64/libtiff.so.3
If not, find whi
The CentOS 4 download works with Ubuntu. Just make sure to get the correct
32 or 64 bit version that matches your operating system. Use uname -m to
tell.
Peace,
Matt.
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Gle
FSL's tools don't use an FA threshold for tractography. So long as there is
a consistent direction(s) to follow it will track through a voxel.
Peace,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Dougla
Hi Doug,
It appears in FreeSurfer 5.0 the flag the bbregister script is looking for
is --fslmat but in the docs it says it is --fsl.
Peace,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Grev
Is it possible to convert an .xfm to an .lta or alternatively to initialize
mri_em_register with an .xfm that one has manually generated? It is not
doing a very good job for me.
Thanks,
Matt.
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Hi Greg,
I think the tracula folks might have gotten their original code from Saad
Jbabdi, but then the code-bases have probably diverged. (My apologizes if
this is not correct!). Here is Saad's publication on global tractography:
http://www.ncbi.nlm.nih.gov/pubmed/17543543/
Peace,
Matt.
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