Re: [Freesurfer] WM edit, remove GM bright rim
Hi Min unfortunately there's not much we can do as these artifacts make the gray matter look just like white matter. Do you see this in many subjects? sorry Bruce On Thu, 17 Mar 2016, Min Liu wrote: Dear Bruce, Many thanks for looking into this. I tried to post orig.mgz to the mailing list yesterday but the email didn't get through because the file size exceeds 1000KB. So I screen-captured two images to showcase the overall quality of T1 and where the problem is. Although the bright rim doesn't occur everywhere, it is mostly seen in the left hemisphere. I hope there is a way to counteract such acquisition defects. Thanks, Min On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischlwrote: Hi Min that looks like it might be a normalization problem. Can you post the orig.mgz and see what it looks like? Is there a bright rim in it also? cheers Bruce On Wed, 16 Mar 2016, Min Liu wrote: Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation. Does anyone know a way to prevent the surface from going out? Thanks, -- Min ___ 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. -- Min ___ 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] WM edit, remove GM bright rim
Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation. Does anyone know a way to prevent the surface from going out? Thanks, -- Min ___ 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.
Re: [Freesurfer] WM edit, remove GM bright rim
Hi Min that looks like it might be a normalization problem. Can you post the orig.mgz and see what it looks like? Is there a bright rim in it also? cheers Bruce On Wed, 16 Mar 2016, Min Liu wrote: Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation. Does anyone know a way to prevent the surface from going out? Thanks, -- Min ___ 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.
Re: [Freesurfer] WM edit, remove GM bright rim
Dear Bruce, Many thanks for looking into this. I tried to post orig.mgz to the mailing list yesterday but the email didn't get through because the file size exceeds 1000KB. So I screen-captured two images to showcase the overall quality of T1 and where the problem is. Although the bright rim doesn't occur everywhere, it is mostly seen in the left hemisphere. I hope there is a way to counteract such acquisition defects. Thanks, Min On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischlwrote: > Hi Min > > that looks like it might be a normalization problem. Can you post the > orig.mgz and see what it looks like? Is there a bright rim in it also? > > cheers > Bruce > > On Wed, 16 Mar 2016, Min Liu wrote: > > Dear Freesufer users, >> We have some T1 images having a rim of bright signal in the GM at some >> spots >> like the one showing in the attached Figure 1. The WM surface goes out to >> include this bright signal and the cortex ends up artificially thin. We >> followed the standard WM edit procedure, which is to erase the bright >> signal >> in wm.mgz. As shown in Figure 2, the bright rim is replaced with >> intensity 1 >> (red). However, that doesn't improve the situation. Does anyone know a >> way >> to prevent the surface from going out? >> >> Thanks, >> >> >> -- >> Min >> >> > ___ > 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. > > -- Min ___ 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.
Re: [Freesurfer] WM edit, remove GM bright rim
Dear Bruce, Thank you very much for your reply. I think we will discard these subjects for the analyses. Thanks, Min On Thu, Mar 17, 2016 at 9:53 AM, Bruce Fischlwrote: > Hi Min > > unfortunately there's not much we can do as these artifacts make the gray > matter look just like white matter. Do you see this in many subjects? > > > sorry > Bruce > > > > On Thu, 17 Mar 2016, Min Liu wrote: > > Dear Bruce, >> Many thanks for looking into this. I tried to post orig.mgz to the mailing >> list yesterday but the email didn't get through because the file size >> exceeds 1000KB. So I screen-captured two images to showcase the overall >> quality of T1 and where the problem is. Although the bright rim doesn't >> occur everywhere, it is mostly seen in the left hemisphere. I hope there >> is >> a way to counteract such acquisition defects. >> >> Thanks, >> Min >> >> On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl > > >> wrote: >> Hi Min >> >> that looks like it might be a normalization problem. Can you >> post the orig.mgz and see what it looks like? Is there a bright >> rim in it also? >> >> cheers >> Bruce >> On Wed, 16 Mar 2016, Min Liu wrote: >> >> Dear Freesufer users, >> We have some T1 images having a rim of bright signal >> in the GM at some spots >> like the one showing in the attached Figure 1. The >> WM surface goes out to >> include this bright signal and the cortex ends up >> artificially thin. We >> followed the standard WM edit procedure, which is to >> erase the bright signal >> in wm.mgz. As shown in Figure 2, the bright rim is >> replaced with intensity 1 >> (red). However, that doesn't improve the situation. >> Does anyone know a way >> to prevent the surface from going out? >> >> Thanks, >> >> >> -- >> Min >> >> >> ___ >> 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. >> >> >> >> >> -- >> Min >> >> > ___ > 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. > > -- Min ___ 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.