I will be out of the country from Jan. 10 - Jan 18, 2011, and will not
have access to email. For issues concerning my laboratory, please contact
my lab manager, Rosa Lafer-Sousa (rlafe...@wellesley.edu).
Thank-you and I'll be in touch when I get back.
Bevil
__
Hi Bruce,
I followed the tutorial at
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial.
I don't really understand why don't the yellow and green surfaces follow the
boundary of wm.mgz, especially the boundary is well
Hi Yang,
Are the slices before and after this slice the same as this one?
> Hi Bruce,
>
> Do you know how to fix it?
>
> Yang
>
> On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
> wrote:
>
>> Then I must be a topologica defect
>>
>>
>>
>> On Jan 10, 2011, at 10:37 PM, Yang Liu wrote:
>>
>> Hi Seb
Not without scrolling through the wm volume. You will need to edit it. Have you
done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu wrote:
> Hi Bruce,
>
> Do you know how to fix it?
>
> Yang
>
> On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
> wrote:
> Then I must b
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
wrote:
> Then I must be a topologica defect
>
>
>
> On Jan 10, 2011, at 10:37 PM, Yang Liu wrote:
>
> Hi Sebastian,
>
> Yes. It is Macaque. There is no aseg.
>
> Yang
>
>
> On Mon, Jan 10, 2011 at 10:15 PM
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu wrote:
> Hi Sebastian,
>
> Yes. It is Macaque. There is no aseg.
>
> Yang
>
>
> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller
> wrote:
> Hi All,
>
>
> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>
> >
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <
sebastian.moell...@rwth-aachen.de> wrote:
> Hi All,
>
>
> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>
> > Does the aseg label that as ventricle?
>
> This pretty much loo
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
> Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is no aseg
for that. I would love to be corrected on that point though.
Best
Sebastian
>
>
>
> On Jan 10, 2011, at 9:
Does the aseg label that as ventricle?
On Jan 10, 2011, at 9:34 PM, Yang Liu wrote:
> Hi Khoa,
>
> Thanks for your reply.
> I attached the snapshot of the same slice with brainmask.mgz. You can see
> clearly that the green and yellow surface at the wrong regions. They doesn't
> look like
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution.
Control points are to fix intensity problem, but you can also add wm
voxels manually to fix any wm defects. In this case, adding that many control
points
Yes, it is accurate. Why do you think it's not? There's lots of
validation stuff on the wiki. The subcortical gray matter structures are
given below.
Left_Thalamus)
Right_Thalamus)
Left_Thalamus_Proper)
Right_Thalamus_Proper)
Left_Caudate)
Right_Caudate)
Left_Putamen
Right_Putamen
Left_Pallidum)
The aseg.stats file takes into account partial voluming which is not
taken into account when you simply sum up the subcortical structures
because some of those structures will be partially volumed with white
matter.
doug
Eisenstein, Sarah wrote:
>
> Hello,
>
>
>
> What goes into the calculat
Hello,
What goes into the calculation of subcortical volume? We have tried adding
volumes of individual subcortical areas but the total does not equal the
subcortical volume provided by aseg. Is the subcortical volume calculation
accurate?
Thanks,
Sarah Eisenstein
_
Hello,
I am working in freesurfer-Linux-centos4_x86_64-stable-v4.0.5-20081003.
The issue I am having started several days ago when I was trying to create
overlap of thresholded stats maps using mri_binarize and mri_concat (from
sig.mgh files). When I was attempting to load the concatenated file I
The current fsfast tutorial does not work with the new version. I'm
preparing a new tutorial. Sorry about that.
doug
Fernanda Palhano wrote:
> Hi,
>
> I am trying to run the FsFast tutorial, but I am getting the following
> error:
>
>
> Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analy
Hi,
I am trying to run the FsFast tutorial, but I am getting the following
error:
Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study]
fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0
-aparc+aseg
tmp: Subscript out of range.
tmp: Subscript out of range.
tmp
I will be out of the country from Jan. 10 - Jan 18, 2011, and will not
have access to email. For issues concerning my laboratory, please contact
my lab manager, Rosa Lafer-Sousa (rlafe...@wellesley.edu).
Thank-you and I'll be in touch when I get back.
Bevil
__
currently it runs in 32b mode. we've had quite a bit of trouble trying
to get the 3rd party libs (tcl/tk/tix/blt and mni) to build as 64b on
the mac (but no problems on linux), which has prevented getting a true
64b mac build going. still working on it
n.
On Mon, 2011-01-10 at 09:01 +0100,
Both of those contrasts will give you the same p-value. The difference
is if you look at the contrast values themselves (gamma.nii). The first
contrast will give you values in units of mm. The second will give you
values in units of 4*mm.
doug
Per Selnes wrote:
> I'm trying to set ut a freesur
I'm trying to set ut a freesurfer group analysis. In my fsgd file there are
four groups/classes and 2 variables, like so:
GroupDescriptorFile 1
Title
Class Class1
Class Class2
Class Class3
Class Class4
SomeTag
Variables Variable1 Variable2
Input subj1 Class1 49 1
Input subj2 Clas
Hi,
The Mac OSX 10.6 version offers the possibility to
run in 64 bits mode (by pressing simultaneously
the 6 and 4 keys during startup).
I was wondering if Freesurfer can be used in 64 bits
mode? In other words: does it use the 64 bits or
does it run only in compatibility mode and in fact
in 32 bi
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