I don't think we have anything yet that will do this for the thalamus. If
you have highres data that is full brain T1 you can analyze it in its
native space in the upcoming 6.0
On Mon, 24 Oct 2016, Dorsa Haji Ghaffari
wrote:
So what I understand is that we can do the segmentation using the whole
brain MRI and then use the higher contrast MRI to refine the thalamus
segmentation? if so, can you explain more about it?
Thank you
Dorsa
On Thu, Oct 20, 2016 at 12:20 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
no, you need full brain coverage in at least one, but we do have
some prototype tools that use a smaller FOV image after a recon
to segment specific structures (including at least a bit of work
on the STN).
As I said though, depending on the details of the 40 slice image
I would be cautious about using it as a gold-standard to
interpret the T1. I would need more information to say for sure
On Thu, 20 Oct 2016, Dorsa Haji Ghaffari wrote:
So basically we have two types of images. One has a
better contrast for seeing the STN to that we can
target it for deep brain
stimulation, but that one is only 40 slices and is
not the whole brain. We have another set of images
which is complete but does
not have a good contrast for showing the
sub-cortical structures. I have attached a sample of
each one. I have also attached my
subject. Does Freesurfer work with only 40 slices?
On Thu, Oct 20, 2016 at 9:51 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Dorsa
if you upload your subject I'll take a look.
What is a 3TC image? I don't know what contrast the
image you sent is
but I would be cautious about only using it to
assess the accuracy of the T1 segmentation
cheers
Bruce
On Wed, 19 Oct 2016, Dorsa Haji Ghaffari
wrote:
I have attached a screenshot of one of
the slices. from what I see it is going a little far
in the
medial and lateral parts. I am using a
3TC image taken by Philips device. Is there any way
to limit the
region of interest before running the
recon-all to only segment the thalamus and may give
better
results?
Thank you
Dorsa
On Wed, Oct 19, 2016 at 5:21 PM, Bruce
Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Dorsa
why do you think it is going out
too far? What intensity volume are you
overlaying it on? Many
segmentations miss the lateral parts of the
thalamus since they have so much
myelin in them
cheers
Bruce
On Wed, 19 Oct 2016, Dorsa
Haji Ghaffari wrote:
> Hi,
> I have done the sub-cortical
segmentation in Freesurfer and have extracted the
left
thalamus, when I put
> it on top of the original MRI,
it seems like it is getting out of the border of
thalamus,
also it is not
> smooth. I wanted to ask if
anyone knows how to limit the computation only to
thalamus, and
also make it
> trace the thalamus more
accurately?
>
> Thank you
>
> Dorsa
>
>
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On Thu, Oct 20, 2016 at 9:51 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Dorsa
if you upload your subject I'll take a look.
What is a 3TC image? I don't know what contrast the
image you sent is
but I would be cautious about only using it to
assess the accuracy of the T1 segmentation
cheers
Bruce
On Wed, 19 Oct 2016, Dorsa Haji Ghaffari
wrote:
I have attached a screenshot of one of
the slices. from what I see it is going a little far
in the
medial and lateral parts. I am using a
3TC image taken by Philips device. Is there any way
to limit the
region of interest before running the
recon-all to only segment the thalamus and may give
better
results?
Thank you
Dorsa
On Wed, Oct 19, 2016 at 5:21 PM, Bruce
Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Dorsa
why do you think it is going out
too far? What intensity volume are you
overlaying it on? Many
segmentations miss the lateral parts of the
thalamus since they have so much
myelin in them
cheers
Bruce
On Wed, 19 Oct 2016, Dorsa
Haji Ghaffari wrote:
> Hi,
> I have done the sub-cortical
segmentation in Freesurfer and have extracted the
left
thalamus, when I put
> it on top of the original MRI,
it seems like it is getting out of the border of
thalamus,
also it is not
> smooth. I wanted to ask if
anyone knows how to limit the computation only to
thalamus, and
also make it
> trace the thalamus more
accurately?
>
> Thank you
>
> Dorsa
>
>
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in error
but does not contain patient information, please contact the sender
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