You're so close! Use fsaverage as the target subject. The output
coordinates will be in MNI305 space.
doug
Jed Singer wrote:
> I'm at my wits' end with what seems like it should be an easy question. I
> have a lot of volume labels that have been saved for a lot of brains. I want
> the Talair
I have been working with Michael Murray on the problems we are having
stripping/segmenting the cerebellum. We have tried various things, including a
range of watershed parameters (1-10), gcut, as well as running these
adjustments in succession (as you suggested below) with various combinations
Hey,
On Fri, Jul 22, 2011 at 02:06:41PM -0400, Michael Waskom wrote:
> We are pleased to announce the 0.1 release of PySurfer, a Python-based
> package for the visualization of surface data from Freesurfer. Please
> see our website at http://pysurfer.github.com/ for information on how
> to instal
Hi Antonella
do you know what the type of acquisition is? That name isn't enough to
know for sure, but it might be.
And yes, you can run more than 1 recon at a time assuming you have enough
ram on your machine. It won't go faster of course unless you have
multiple cpus
cheers
Bruce
On Fri,
Dear Bruce,
I have two more questions for today, please:
1). Just to be sure that I understood correct: for my cortical thickness
studies and also for a group studies analysis I will use only the data from
the 3DAx_T1series which was converted to a .nii.gz file. Is this right?
2). If I want
hi mike,
In theory it could, as we use Nibabel for i/o and they support Gifti.
> However, I have no data in Gifti format at the moment to work with, so
> at the moment I would say we are Freesurfer specific.
>
freesurfer does support giftis.
mris_convert --combinesurfs fsaverage/surf/lh.inflated
Hi Matt,
In theory it could, as we use Nibabel for i/o and they support Gifti.
However, I have no data in Gifti format at the moment to work with, so
at the moment I would say we are Freesurfer specific.
Best,
Michael
On Fri, Jul 22, 2011 at 2:09 PM, Matt Glasser wrote:
> Hi Michael,
>
> Out of
I'm at my wits' end with what seems like it should be an easy question. I have
a lot of volume labels that have been saved for a lot of brains. I want the
Talairach coordinates corresponding to those points. It seems like
mri_label2label should be able to do this, by putting in 'talairach' as th
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] On
Dear Freesurfers,
We are pleased to announce the 0.1 release of PySurfer, a Python-based
package for the visualization of surface data from Freesurfer. Please
see our website at http://pysurfer.github.com/ for information on how
to install the package and a gallery of examples. We hope you'll fi
Dear list,
I got an error after following the newer version of the longitudinal
stream 5.1.
long_mris_slopes worked without problems for my data which was
longtudinally processed in 4.5.
I also split the qdec.table to the cross for being able to be loaded
in qdec GUI.
Somehow I got the error th
Hi Antonella,
no, you pick *one* file in each series (it doesn't matter which one,
mri_convert will figure out the rest), and do something like:
mri_convert 1.3.46.670589.11.17385.5.0.8952.2011042600464496394.dcm
3DAx_T1.nii.gz
the only one(s) FreeSurfer will use are the 3D T1-weighted scan
Dear Bruce,
I am a little confused and I will be very grateful if you can make it a little
more clear:
So I start converting the dicom files from 3DAx_T1 (having the first file
called 1.3.46.670589.11.17385.5.0.8952.2011042600464496394) series by running:
mri_convert 2011042600464496394.dcm
Hi Kevin - This is unfortunately a problem with the macos freesurfer
distribution, which is still built on leopard instead of snow leopard b/c
of compatibility issues with some libraries unrelated to tracula. It's
possible to compile tracula on snow leopard (in fact that's what I use)
but you
Freesurfer users,
I have ran into a malloc error running trac-all. Looks like the same error
that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted.
It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using
trac-all –prior –c dmrirc.txt with the sa
Hi Jixin,
mris_make_face_parcellation uses an icosahedral sampling, so you cannot use
it with an arbitrary annotation, and the parcels in it will not correspond
to the brain regions in any of the annots but rather will cut across
boundaries. You could certainly use matlab for example to compil
Dear FS experts,
Freesurfer could provide for every participant a standardized partition
of the cortex into 66 regional areas. My aim is to use freesurfer to
subdivide these regional areas into a set of small and compact regions,
resulting in high resolution atlas covering the entire cortex (t
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