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 <fischl@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 <fischl@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 <fischl@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 <fischl@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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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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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
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