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 >> > >> > >> _______________________________________________ >> 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 <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 >> > >> > >> _______________________________________________ >> 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. > >
_______________________________________________ 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.
