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
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
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:
on a
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 way to convert from one to the other? What
about
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
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,
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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Glasser
Cc
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e.
David) think the problem with Rouhi's data is that FreeSurfer did not detect
that the original images were tipped forward 90 degrees and as a result the
surface registration failed intermittently (i.e. in some subjects it
Zero probably means no label.
Peace,
Matt.
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Forrest Sheng
Bao
Sent: Sunday, July 31, 2011 3:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] label value 0
There are different numbers of vertices in subjects surfaces. It is
possible to resample subjects' surfaces to a common mesh after registration,
but the FreeSurfer folks don't prefer this approach. They prefer to simply
resample the quantitative data.
Peace,
Matt.
-Original Message-
Hi Michael,
Out of curiosity, does this also support the GIFTI format? If so, one could
use it to view surface data from a wide variety of software packages.
Thanks,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
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.
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.
___
Freesurfer mailing list
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
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
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
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
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
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 that the nodes are all lined up? I am
. When the sphere.reg 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
. 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 Doug and Bruce,
I am somewhat surprised by your responses
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
.
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 the monkey
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
On Thu
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
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
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
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 fah...@sun.ac.za
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
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 volume name switch to reslice like a template
Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space
without Resampling
It depends on the resolution.
On Aug 23, 2009, at 6:53 PM, Matt Glasser m...@ma-tea.com wrote:
Hi Bruce,
Presumably all that was done to the volume when it was imported was
that
some zero
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:
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