Hi,
On an Intel Mac the Edit Voxels Tool does not work,
contrary to a PPC Mac.
This applies both to version v4.3.1 and v4.5.0.
Ed
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Dear all,
We have created our own atlas based on several subjects. We have the atlas
in analyze volume files and would like to know if we can somehow convert
these files into the .gcs format without having to go through all the manual
steps of creating a template and labels.
Thanks,
Pernille
Hi Pernille,
do you mean for surface parcellation or volume segmentation? It's not
really conversion, it's training using either mris_ca_train or
mri_ca_train.
cheers
Bruce
On Wed, 7 Apr 2010, Pernille Iversen wrote:
Dear all,
We have created our own atlas based on several subjects. We
Hello,
I am trying to check if some talairach coordinates of AI (auditory primary)
(from paper) are in the transverstamporal label, on am subjects. To do this,
and thanks to your answers I used the commands line in tksurfer:
select_talairach_coordinate x y z
mark_vertex $select 1
and I can
I guess you could put it in a tcl script invoked from within a shell
script, then parse out the answers from the output, but I don't know an
easier way to do it, sorry.
Bruce
On Wed, 7 Apr 2010, Ben Hamida Cammoun Leila Faiza wrote:
Hello,
I am trying to check if some talairach coordinates
Hi Jan,
how will you ever know left from right? You can use the various options
in mri_convert to tell it what the image orientation is, but you must be
very careful not to introduce a left/right flip.
cheers
Bruce
On Tue, 6 Apr 2010, Janani
Dhinakaran wrote:
Hello,
I was wondering whether
Hi Vadim,
sometimes there is a single edge left when you make the cut that connects
across it. Can you zoom in and check? Usually this is easiest if you
overlay the wireframe. You can also try dilate cuts and flatten to see if
that removes the problem, although you will lose another mm of
Hi,
I am still curious whether and how the above mentioned feature could be
implemented into optseq2.
I would be delighted and very greatful to hear your ideas.
Cheers,
Tilman
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hi
aside from new ROIS (i.e. the cingulate being divided into 3 parts), the
2009 looks like it has smoother/different boundaries than the 2005 one, even
for ROIs that remain the same as the 2005. what is that a result of?
thanks, frida
--
Frida E. Polli, PhD
Postdoctoral Fellow
Brain
Frida,
see this page for changes:
https://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges
there's an HBM poster linked there as well. not sure when the paper is
due.
n.
On Wed, 2010-04-07 at 10:54 -0400, Frida Polli wrote:
hi
aside from new ROIS (i.e. the cingulate being
Hi Frida
I'm afraid I won't have any anatomical explanation for this smoothing,
since most of the boundaries remained the same on the surfaces of the
subjects used to train the atlas. I don't know if any minor changes
occured in the labelling algorithm between these 2 versions ; maybe
Bruce
Hi Frida,
we model filter the output a 10 times by default. Not sure if this
changed between versions, but it is the smoothing we do. You can change
it by specifying the number of iterations with -f # of iters to
mris_ca_label.
cheers
Bruce
On Wed, 7 Apr 2010, Christophe Destrieux wrote:
Hi
Hi Sherri,
one of the control points seems to be in gray matter, which is probably
causing this. Please try deleting it and rerunning autorecon2-cp.
Sita.
On Tue, 6 Apr 2010, Sherri Novis wrote:
Hello brilliant and generous FS people,
I have introduced a problem I cannot solve. I am
Thanks Sita. I have struggled with how to capture very ghostly gray matter.
Sometimes throwing a CP in it works (I understand now this may be hosing it
sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces
to capture all the gray - is the only way to capture the ghostly
Hi Sherri,
you may also have a topological defect near those control points, which
is causing the surfaces to lose the wm (and hence the gm also). What does
the wm.mgz look like there? Is the wm segmented correctly but not
included in the ?h.orig surface? If you upload this data we can take a
Thank you Bruce. I've had this prob randomly before - but recently it's been
each of the last 10 datasets - so I think its a process issue that I introduced
- but would love help from any direction.
If I use the upload site - which files to you need? will send wm.mgz, ?h.orig
surface - any
Hello, Freesurfer experts:
I noticed for analyzing the results from autorecon2, the intracranial volume
are controlled as covariate in some publications. Is there any corresponding
covariate for cortical results from autorecon3, cortical thickness, surface,
and volume?
In my current
:
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Hi Karl,
you could try including average cortical thickness over the entire
hemisphere as a covariate. This was Mike Harms' suggestion, and I think a
good one.
cheers
Bruce
On Thu, 8 Apr 2010, Liukarl wrote:
Hello, Freesurfer experts:
I noticed for analyzing the results from
Dear Freesurfers,
I just tried to use mri_motion_correct.fsl with the -tmpdir and -nocleanup
options. Since I currently average around 10 to 16 mprage volumes per subject
(NHPs) I want to look at the variance in addition to the average. And it seemed
simplest to just keep the co-registered
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