External Email - Use Caution Awesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Hi All, as some of you have figured out, we have a beta version of FS > 8.0.0. Please give it a spin and let us know if you have any problems or > concerns. > > The release notes are here > https://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGXN5dFVNHJpGgR0en61nEygdqxr_r1Wc2lzTP8tMxj2Mm5Kd12legZwYkmuUNI6W1pV128FFEKR50sXw0SWoAhimRb0wA4zNSb8vHOLda-h3SFtiXHW3UijR_Q2VNWxXg9Mf_u2QEuTxw6FSxJfmShpM3jaSD_K-mKrVmEKpykxD0152nXBL4MJ2LBp6Rio8mv0TzalahFHdHUqcEqnNmqL-1p1v1D3WuBFgM7CaT1LKZ5UQdNaQRKtd65tOkK2y1wIdk-WpFqLJknkohHGN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes > which I have > copied below. > One bug that we have already found is that you must set environment > variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or > setenv FS_ALLOW_DEEP 1 (for csh/tcsh) > > thanks > doug > > - > > Now uses SynthSeg > <https://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg>, > SynthStrip > <https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io>, > and SynthMorph > > <https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io> > (deep learning algorithms). These make > recon-all more robust and much faster. Technically, SynthMorph > > <https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io> > is not needed for recon-all to run, but the > nonlinear registration can be used in multimodal analysis to map to the > MNI152. > - There is now DL automatic segmentation of regions that often cause > errors in pial surface placement. These include the major sinuses (sagittal > and transverse) as well as a spot between frontal and temporal lobes where > the middle cerebral artery (MCA) and dura cause bright areas. > - Several fixes in entorhinal cortex. First, the WM in EC is segmented > using DL. The WM is often only 0.5mm thick and very hard to see; this often > resulted in severe white surface areas in this location requiring manual > editing to fix. The new surface now represents gyrus ambiens much better. > Second, The white surface is extended to the front of amygdala. Third, the > binary cortex of label now covers entorhinal cortex and parts of the > temporal pole better allowing the pial surface to extend out to its true > edge. > - Some bugs where found in and around inferior frontal cortex causes > the white surface to extend too far into basal ganglia. This has been > fixed. This is above and beyond the issue reported in 7.3.2 below. > - All the bug fixes described below are now turned on by default. > - These changes will work with longitudinal with the caveat that the > volumetric segmentation will not be fully longitudinal. The segmentation > will be applied to the time point in the base space, but it will not (and > cannot) be initialized with the base segmentation. Initial tests indicated > that the change in power was minimal and mixed. > - recon-all will now run in about 2h vs 8h on a single CPU. It will, > however, required about 24GB of memory to run. > - > > The use of SynthStrip > <https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io> > should make recon-all > much more robust as the old skull stripping method often included extra > cerebral tissue. > - With synthseg, we are now supplying a segmentation-based total > intracrainial volume (sTIV) along with the registration-based estimated TIV > (eTIV) > - We have applied v8 to several studies (aging, AD crossectional, AD > longitudinnal, schizophrenia). There were no major changes in the ability > to detect effects, and there was no interaction between effect and version. > But let us know how it performs on your studies. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozjmE8B5STLMyZau0HLaBHVV4DMkawFTOxb7I_n7YG5CHXME6vnOLzeoNfsRSy0WjvCS_7sBSnH6j9uoqgf-ciQKbBFcXYp76dnbQpP6qcq9canmI5nCYx_3Avp4OG5s65PvcuNoHYnp8vzrDuTEV78cdvD712MAKtOzc8xDnCKn1fQcF8Or0c-_LGPrhcZz3NJdDx-5uWhnoIplcNeo9dWAlVnrAHj8temxnWbTP4lDBAT428ldCflGSLB1bAOccs6Xg3Z0zVztaGXuZYaPF/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 > https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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