and mri_morphology which has a dilation operator in it
On Mon, 16 Aug 2010,
Douglas Greve wrote:
> you can also use mri_binarize which has a --dilate option. I think it
> dilates if it has one or more faces in common. You might also look into
> fslmaths (you can easily convert from mgz to nifti)
you can also use mri_binarize which has a --dilate option. I think it
dilates if it has one or more faces in common. You might also look into
fslmaths (you can easily convert from mgz to nifti) if that's an issue
On 8/16/10 8:46 PM, Bruce Fischl wrote:
> Hi Jeff,
>
> you are welcome to our sou
Hi Jeff,
you are welcome to our source code which has region-growing algorithms in
the volume (e.g. for control point detection) and on the surface.
cheers
Bruce
On Mon, 16
Aug 2010, Eriksen, Jeffrey (Portland) wrote:
> Bruce,
>
> Yes, you are likely correct, but my boss wants to do it this w
Bruce,
Yes, you are likely correct, but my boss wants to do it this way.
Besides, I am going to have other uses for region growing that you might
find scientifically acceptable. But the question still stands - does
Freesurfer give me access to such a basic tool, or will I have to write
my own with
Hi Alan,
which curvature index do you mean?
Bruce
On Mon, 16 Aug 2010, Alan Francis wrote:
> Hi All:
>
> Does a lower score on the curvature index of the CC (as done by FreeSurfer)
> imply that the Corpus Callosum is more curved (smaller radius) or is it the
> other way around?
>
>
> thank you,
Hi Nick,
On Aug 16, 2010, at 14:47 , Nick Schmansky wrote:
> sebastian,
>
> snow leopard has given us a number of headaches in the freesurfer gui
> department, and it may take a while to sort them out. the gray scale
> issue is one of them. freeview not working is another.
Ah, too ba
you don't need to do anything special. Version 5 will see the edits and
keep them (though it is a good idea to back up your data just in case:).
Mira Michelle Raman wrote:
> Hi,
> I want to re-run subjects in 5.0 that have been
> edited in 4.5(wm.mgz, brainmask.mgz, control points).
>
> Wha
Hi,
I want to re-run subjects in 5.0 that have been
edited in 4.5(wm.mgz, brainmask.mgz, control points).
What command should I use to preserve these edits?
-Mira
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sebastian,
snow leopard has given us a number of headaches in the freesurfer gui
department, and it may take a while to sort them out. the gray scale
issue is one of them. freeview not working is another.
n.
On Mon, 2010-08-16 at 11:35 -0700, Sebastian Moeller wrote:
> Hi Nick,
>
> pretty coo
There is a new retinotopic mapping stream. I have not fully documented
it yet. You now analyze the retinotopy data like you would other
functional analysis in fsfast. First create an "analysis" with
mkanalysis-sess. Run it with -help to get info on retinotopy-specific
parameters. Eg,
# Create
This is very nice. I just tried to do an analysis in the new release under
Mac OS X (10.6.4, Intel). However, retinotopic mapping would not run. I did
"sfa-sess -a rtopy -sf sessid -df sessdir". The error message says
"sfa-sess: Command not found." Any idea why this is the case? Thanks.
-Yuhong
O
It's almost flat. So the radius is very large.
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
On Mon, Aug
Hi All:
Does a lower score on the curvature index of the CC (as done by FreeSurfer)
imply that the Corpus Callosum is more curved (smaller radius) or is it the
other way around?
thank you,
Alan
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan Francis
Brain Spectroscopy and Neuroimaging La
yes, but dont mix results from different versions if conducting a group
study.
n.
On Mon, 2010-08-16 at 21:29 +0200, Diederick Stoffers wrote:
> Hi all,
>
>
> Can I simply rerun recon-all -s -all on datasets already processed in
> a previous version?
>
>
> Cheers,
>
>
> Diederick
>
>
>
>
Try mri_surfcluster
doug
Pye, Brandon (NIH/NIMH) [F] wrote:
> Hi all,
>
> I have a question about performing a cluster correction. I have gone through
> the Group Analysis tutorial on the FsTutorial website, but it walks through
> the process of doing a glm analysis to compare different conditi
Hi all,
I have a question about performing a cluster correction. I have gone through
the Group Analysis tutorial on the FsTutorial website, but it walks through the
process of doing a glm analysis to compare different conditions of data. I
have a mask file (.mgh) that contains activation leve
Hi all,
Can I simply rerun recon-all -s -all on datasets already processed in a
previous version?
Cheers,
Diederick
On 16 aug 2010, at 18:04, Nick Schmansky wrote:
> Announcement!
>
> There is a new release of FreeSurfer, v5.0.0!
>
> Features and fixes are described in the ReleaseNotes pag
Hi Nick,
pretty cool. It looks like this is the real deal :). I noticed something weird
on macosx 10.6.4 (x86_64 kernel). The simple inflated surgace is not rendered
smoothly but shows recognizable steps in the gray values. Attached an png
showing the effect (I hope this is small enough to make
Announcement!
There is a new release of FreeSurfer, v5.0.0!
Features and fixes are described in the ReleaseNotes page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
It is available for download at:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Please pose questions about
Mike is correct. Thanks Mike!
doug
Michael Waskom wrote:
> Hi Heidi,
>
> You can use mri_segstats on the surface. You can either use the
> --label option or, if you have a lot of labels, you can merge them
> into an annotation with mris_label2annot and then use the --annot
> option to extract
Hi Heidi,
You can use mri_segstats on the surface. You can either use the --label
option or, if you have a lot of labels, you can merge them into an
annotation with mris_label2annot and then use the --annot option to extract
from all at once (values are extracted from each region separately; this
Hi,
Last year, I have been working for four months with David Salat and so, I have
learnt a lot, including the dt_recon command.
>From David, I also learnt to use mri_segstats command in order to get minimum
>p-values for each label in my volume.
However, now I have performed cortical thickness
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