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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 volumeare 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 haveextracted 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 > > _______________________________________________ Freesurfer mailing list 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.
Freesurfer mailing list 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.
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 volumeare 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 haveextracted 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list 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.
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 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 > > _______________________________________________ Freesurfer mailing list 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.
Freesurfer mailing list 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.
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 > > _______________________________________________ Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 fischl@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 fischl@nmr.mgh.harvard.edu wrote: Hi Dorsa
if you upload your subject I'll take a look. What is a 3TC image? Idon'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 whatI 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? Whatintensity 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 inFreesurfer 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list 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.
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? Idon'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 whatI 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? Whatintensity 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 inFreesurfer 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 fischl@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 fischl@nmr.mgh.harvard.edu wrote: Hi Dorsa
if you upload your subject I'll take a look. What is a 3TC image? Idon'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 whatI 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? Whatintensity 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 inFreesurfer 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for theperson 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.
Freesurfer mailing list 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.
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? Idon'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 whatI 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? Whatintensity 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 inFreesurfer 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 fischl@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 <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 > > _______________________________________________ Freesurfer mailing list 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. _______________________________________________ Freesurfer mailing list 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. 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 > > _______________________________________________ Freesurfer mailing list 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. _______________________________________________ Freesurfer mailing list 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.
Freesurfer mailing list 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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Dorsa Haji Ghaffari