I think this should work, though it might exit early due to the bug that
I just posted. But a fixed version should be able to do this.
On 11/7/2024 2:37 PM, Aaron Tanenbaum wrote:
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 *MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
<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.
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