Re: [Freesurfer] Dura classified as GM in brainmask
Hi Bruce, Thank you for your reply. I am using 5.3.0 version. Do I still only correct misclassified GM voxels in the brainmask? For the subjects with brain classified as cerebral cortex in the aseg file which is outside of the pial surface (but present in the brainmask) how do I correct this: 1. If it should be GM how do I edit the pial surface? 2. If it is non-brain matter how do I remove it from the aseg file- do I erase these voxels from the brainmask even though they are not in the pial surface mask? Thanks, Ciara Hi Ciara what version are you running? I think you only need to correct voxels that cause the white and/or pial surfaces to be incorrect, as we correct the aseg with them (at least I think we do in v6) cheers Bruce On Wed, Dec 13, 2017 at 12:11 PM, FSL Analysis wrote: > Hi again, > > I realize my last question about the brainmask did not make sense. I meant > to ask if I have to either manually delete all non-brain voxels around the > eye area which is very time consuming per subject or just delete those > misclassified as GM? ( I check this through the command: tkmedit > subj_output brainmask.mgz -aux T1.mgz -surfs) > > Also for some subjects: > 1. When I open freeview and look at the aseg file there is area around the > eye misclassified as cerebral cortex for some subjects. > 2. When I load the pial surface the aseg file shows cerebral cortex in the > temporal poles and frontal lobes near the eye region outside of the pial > surface outline. How do I edit this? > > > > I look forward to your response. > > > > > Thanks > > On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis > wrote: > >> Hi all, >> >> I have processed data using freesurfer and the output for most of my >> subjects did not remove all of the eye and dura around it during skull >> stripping. When I check the brainmask there is dura (or blood vessel) in >> the frontal lobe that is classified as GM. >> >> I am wondering if I have to manually edit the skullstrip and rerun >> recon-all or do I just edit the brainmask file by deleting non-brain >> voxels? Or do I have to do both? >> >> If I only edit the brainmask file does this skip any other important >> processing steps that may affect my results? >> >> I am planning on looking at brain volumes and cortical thickness and how >> they relate to behavioral measures. >> >> >> >> >> Kind Regards, >> >> Ciara >> > > ___ 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] Dura classified as GM in brainmask
Hi Ciara what version are you running? I think you only need to correct voxels that cause the white and/or pial surfaces to be incorrect, as we correct the aseg with them (at least I think we do in v6) cheers Bruce On Wed, 13 Dec 2017, FSL Analysis wrote: Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through this command: tkmedit subj_output brainmask.mgz -aux T1.mgz -surfs) Also for some subjects: 1. When I open freeview and look at the aseg file there is area around the eye misclassified as cerebral cortex for some subjects. 2. When I load the pial surface the aseg file shows cerebral cortex in the temporal poles and frontal lobes near the eye region outside of the pial surface outline. How do I edit this? I look forward to your response. Thanks. On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis wrote: Hi all, I have processed data using freesurfer and the output for most of my subjects did not remove all of the eye and dura around it during skull stripping. When I check the brainmask there is dura (or blood vessel) in the frontal lobe that is classified as GM. I am wondering if I have to manually edit the skullstrip and rerun recon-all or do I just edit the brainmask file by deleting non-brain voxels? Or do I have to do both? If I only edit the brainmask file does this skip any other important processing steps that may affect my results? I am planning on looking at brain volumes and cortical thickness and how they relate to behavioral measures. Kind Regards, Ciara ___ 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] Dura classified as GM in brainmask
Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through the command: tkmedit subj_output brainmask.mgz -aux T1.mgz -surfs) Also for some subjects: 1. When I open freeview and look at the aseg file there is area around the eye misclassified as cerebral cortex for some subjects. 2. When I load the pial surface the aseg file shows cerebral cortex in the temporal poles and frontal lobes near the eye region outside of the pial surface outline. How do I edit this? I look forward to your response. Thanks On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis wrote: > Hi all, > > I have processed data using freesurfer and the output for most of my > subjects did not remove all of the eye and dura around it during skull > stripping. When I check the brainmask there is dura (or blood vessel) in > the frontal lobe that is classified as GM. > > I am wondering if I have to manually edit the skullstrip and rerun > recon-all or do I just edit the brainmask file by deleting non-brain > voxels? Or do I have to do both? > > If I only edit the brainmask file does this skip any other important > processing steps that may affect my results? > > I am planning on looking at brain volumes and cortical thickness and how > they relate to behavioral measures. > > > > > Kind Regards, > > Ciara > ___ 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] Dura classified as GM in brainmask
Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through this command: tkmedit subj_output brainmask.mgz -aux T1.mgz -surfs) Also for some subjects: 1. When I open freeview and look at the aseg file there is area around the eye misclassified as cerebral cortex for some subjects. 2. When I load the pial surface the aseg file shows cerebral cortex in the temporal poles and frontal lobes near the eye region outside of the pial surface outline. How do I edit this? I look forward to your response. Thanks. On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis wrote: > Hi all, > > I have processed data using freesurfer and the output for most of my > subjects did not remove all of the eye and dura around it during skull > stripping. When I check the brainmask there is dura (or blood vessel) in > the frontal lobe that is classified as GM. > > I am wondering if I have to manually edit the skullstrip and rerun > recon-all or do I just edit the brainmask file by deleting non-brain > voxels? Or do I have to do both? > > If I only edit the brainmask file does this skip any other important > processing steps that may affect my results? > > I am planning on looking at brain volumes and cortical thickness and how > they relate to behavioral measures. > > > > > Kind Regards, > > Ciara > ___ 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] Dura classified as GM in brainmask
Hi all, I have processed data using freesurfer and the output for most of my subjects did not remove all of the eye and dura around it during skull stripping. When I check the brainmask there is dura (or blood vessel) in the frontal lobe that is classified as GM. I am wondering if I have to manually edit the skullstrip and rerun recon-all or do I just edit the brainmask file by deleting non-brain voxels? Or do I have to do both? If I only edit the brainmask file does this skip any other important processing steps that may affect my results? I am planning on looking at brain volumes and cortical thickness and how they relate to behavioral measures. Kind Regards, Ciara ___ 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.
