External Email - Use Caution Many thanks. This really helps. My best AJ
On Mon, Apr 26, 2021, 02:21 Stefano Cerri <s...@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-vfbZR3wVTBOWsjJ3Dpkhl8uYSJ4t-uvJ76fmq7gIt7rNQtluL7gk_Z08Jk5Gl_mGN6p4XNtpZNFOvpgJbyohBtm-9AC9mq-g8P5QFuKFI0ZONvb_VIapxucwVpfV0hqe8b-0GNi3Rc9rxXQPc40rDqwfd_kmdtPsK5CUw_fdQV19Vz_B1_15P6J7co11JfjNURHBO-sBdLgAr1UwxtxFHa_YZOlO9xunFdk8WRyRSdtpWQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg)? > 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 <ajcns1...@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 <dgr...@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 >> listfreesur...@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_a51HyAUq1TZfJaXW8cU7pRImM7LiUy8STiXpcD5v_OQM59I4aFaouqZ1N7OknJTOqaaTP-AZZfbQHhPbTtEGLSf3q7b6xzzYo5fSWMmknXJ-VKJeC_9tdMIn3ve1Z59jRX6Kn4knwn0hA2tG4U6CSEtUPe7xkaxpVeADJHwhZIAb5vNuLPRwpF6QhoGzfhHYck_j1EvMjFDWXhf5fbiy6jZ9Aa4w2PRN0-JvP7sY3PY_mFSDcCBWVGZ0dgzPov_rPV3AmCUw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> 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-6ifINShVIeB7LXmhUw0DCmWcVTzMDW75qCpBeSCgybdX2qEC4f5Qn57xl4f2UuCiMBfmaaDGp9zF-JCvZrA0D_Gj2ekDbP2UCr8pqTJPkdCKN2p5PTBpkD_Y0mYDbttQKJW9T2Wr1MUH7PIBBNgTwBbG8FWIeI3FwSqdV_n5UKI1b6_9_6ctqepbsLfglVWRoBC3bfk-9ADjSqiwCWru4KsYt9xffbZSXoXgKeA5TbPQQJt5ldK83UDWmcG7ZEKgrAa5yUEA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> . 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. >> >
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