External Email - Use Caution
Hi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?
Can --eTIV be added to SAMSEG?
In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?
Can corpus callosum be segmented separately in Samseg?
Sorry for all the questions.
Many thanks.
On 4/24/2021 5:56 PM, AJ wrote:
External Email - Use Caution
Hi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?
I'll let Stefano (cc'ed) weigh in.
Can --eTIV be added to SAMSEG?
Not sure what you mean here. There is an etiv value that is output in the samseg folder
In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?
No, not yet
Can corpus callosum be segmented separately in Samseg?
I have not tried this, but you can try mri_cc -aseg seg.mgz -o seg.cc.mgz
Sorry for all the questions.
Many thanks.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Many thanks. Best. AJ
On Sun, Apr 25, 2021, 21:45 Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 4/24/2021 5:56 PM, AJ wrote:
External Email - Use CautionHi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?
I'll let Stefano (cc'ed) weigh in.
Can --eTIV be added to SAMSEG?
Not sure what you mean here. There is an etiv value that is output in the samseg folder
In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?
No, not yet
Can corpus callosum be segmented separately in Samseg?
I have not tried this, but you can try mri_cc -aseg seg.mgz -o seg.cc.mgz
Sorry for all the questions.
Many thanks.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1l9MNqSBi0fie5JCEbRxuCBooWaZ9TWelHWYkUnVO0kk2xZ... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/18603MHVkU24BOgwa-QtqkOB5hOy9G_Wx-VEc65dNFLRu0SA... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Hi AJ,
Did you already use the --lesion-mask-pattern flag for the T2 contrast (Cf. https://secure-web.cisco.com/1_LCeYfRehXKnxqg96wNDurvB9Z24rRz-AYFwjNiTlLrgbp... The default behavior will mask lesion voxels with respect to the cortical gray matter, but you can also try to relax the constraint by masking them with respect to the white matter (you need to include the flag --lesion-mask-structure 'White').
Also, instead of trying different --threshold flags, you can save segmentation maps with the flag --save-posteriors and check the lesions map at /yourOutput/posteriors/Lesion.mgz. This volume will give you a rough idea of which threshold is the most suitable.
If lesions are still not segmented well, as last resort you can always manually edit them from the seg.mgz.
Hope it helps.
Best, Stefano
________________________________ From: AJ ajcns1969@gmail.com Sent: 26 April 2021 04:52 To: Freesurfer support list Cc: Stefano Cerri Subject: Re: [Freesurfer] T2 lesion editing
Many thanks. Best. AJ
On Sun, Apr 25, 2021, 21:45 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
On 4/24/2021 5:56 PM, AJ wrote:
External Email - Use Caution
Hi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them? I'll let Stefano (cc'ed) weigh in.
Can --eTIV be added to SAMSEG? Not sure what you mean here. There is an etiv value that is output in the samseg folder
In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all? No, not yet
Can corpus callosum be segmented separately in Samseg? I have not tried this, but you can try mri_cc -aseg seg.mgz -o seg.cc.mgz
Sorry for all the questions.
Many thanks.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1tF2sXr9JqGRqdIXsxeQ3Ompts5J_oMOX5PqbkraJ8do6LR...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1tF2sXr9JqGRqdIXsxeQ3Ompts5J_oMOX5PqbkraJ8do6LR... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1xo60oE9X87WycXPP0hXU5ymmWZYbNzsodeulNQFxImsQHLU... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Many thanks. This really helps. My best AJ
On Mon, Apr 26, 2021, 02:21 Stefano Cerri stce@dtu.dk wrote:
Hi AJ,
Did you already use the *--lesion-mask-pattern *flag for the T2 contrast (Cf. https://secure-web.cisco.com/1Nr9ikQiL70M1xJaljJ-ChTPoG2jOGZUYBEWZ8Wn-vfbZR3... The default behavior will mask lesion voxels with respect to the cortical gray matter, but you can also try to relax the constraint by masking them with respect to the white matter (you need to include the flag *--lesion-mask-structure 'White'). *
Also, instead of trying different --threshold flags, you can save segmentation maps with the flag *--save-posteriors *and check the lesions map at /yourOutput/posteriors/Lesion.mgz*. *This volume will give you a rough idea of which threshold is the most suitable.
If lesions are still not segmented well, as last resort you can always manually edit them from the seg.mgz.
Hope it helps.
Best, Stefano
*From:* AJ ajcns1969@gmail.com *Sent:* 26 April 2021 04:52 *To:* Freesurfer support list *Cc:* Stefano Cerri *Subject:* Re: [Freesurfer] T2 lesion editing
Many thanks. Best. AJ
On Sun, Apr 25, 2021, 21:45 Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 4/24/2021 5:56 PM, AJ wrote:
External Email - Use CautionHi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?
I'll let Stefano (cc'ed) weigh in.
Can --eTIV be added to SAMSEG?
Not sure what you mean here. There is an etiv value that is output in the samseg folder
In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?
No, not yet
Can corpus callosum be segmented separately in Samseg?
I have not tried this, but you can try mri_cc -aseg seg.mgz -o seg.cc.mgz
Sorry for all the questions.
Many thanks.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Zb5M2DW3mfUYj_a51HyAUq1TZfJaXW8cU7pRImM7LiUy8S... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1lIYzjYqBo16WL-6ifINShVIeB7LXmhUw0DCmWcVTzMDW75q... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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