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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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