Not sure. Does it have access to as much memory as it wants? Can you send the log file?
On 11/25/2024 1:29 PM, Martin Kavec wrote: > External Email - Use Caution > > Hi, > > I am giving a try to FS 8-beta, but I am not seeing such a speed up as > in the release notes: 2 hours and 24 GB of memory. In my case a case > runs on average in 4.5 - 5 hours. Also I do not see such a high > demands for memory, which could be related to speed. > > Besides t1 I also have t2 as input. Could this have an influence? I > have 24-core CPU, 96 GB RAM, 24 GB GPU running on Ubuntu 24. > > recon-all -all -s sub_fs -i ./sub/mri/orig/001.nii.gz -T2 > ./sub/mri/orig/T2raw.nii.gz > > Thanks, > > Martin > > On Thu, Nov 7, 2024 at 6:54 PM 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/1WZjdr8LjQY4Je-aSRZUkzxn05p-5a_0hVrm6R-DwjleJe2qgDxRsCFRQfBszP2zaSnI0nBDAiNBpP2wCEESI3ZV63zJH021paEFmNPDRVKOjiLWu7AbtNNKMtglKc7THahfoThc3BtRLZ6eDxv6kNmvfBbby2bmNx9pNXdLR5WhQDTvND9qWgGL7d8OrdRhwME7DLFplrfpyd-8P-8K_AMb3nTvUbXlTc4NKcmg7Ya54zrbF984s7ViKvCdxUk9vJSFXWBW2b9TL0LCjpEa0egue-d8O7eKOAC2C8Fc2Xz2ni63VIJSUXCQfEpXMwx4Q/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, SynthStrip, and SynthMorph (deep learning algorithms). >> These make recon-all more robust and much faster. Technically, SynthMorph 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 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/1ng-lb9IRCeQMllO5GufVHweINjiZZcKqOzjzTLPh3F1U37MOHCD9mEzdn06PAdzOWrIUslzhepGy4Sdm9y-yU4SvEI4TofIfibG13zDksVNNtjurHYzppIKTyrejwogixAYgwUng4CD8QFOw_H7b9hrfuE4LmA4G5NTicthepDeo-YsrKPwhZeuN2XamlUcO-3b1ttKEaC99QSPrSaYEwznPts_COue0xQzMFmVB4FKDqYfYNStrBuNuPCk8Uh-W-U-PaRmpaF5lKh9jMzTJ-jT7UklU2GvZtUmqp1U_6H4W8ozDzVAJ2RZCJ2SAtESW/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/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9ZsFJkCoaK-ypoV27laWA8-QXySl1rs6Ix8g1lWftpt34Qi_1jyrnx0aF-nAwE1-dMJPhDA71fGn_uS-Pr1qp7N9CPcGp04o6qjnkPpDeRrZRPd9zXQgI7fhEJxwuOOsGIjg0bkwGO0cH9JsBlNZTVvK8ddA4bFRpYCvYzmz5CGr-Sn8c6bxHwt7h2oyQL35LKlh2FROn5kHnl-xe1c6VeswzZRQYtBi4qorpJDOrWHjMagobwL8KThaAEO4YAIPq8n2fcAt3_kasI5FXjDI/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> >> <https://secure-web.cisco.com/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9ZsFJkCoaK-ypoV27laWA8-QXySl1rs6Ix8g1lWftpt34Qi_1jyrnx0aF-nAwE1-dMJPhDA71fGn_uS-Pr1qp7N9CPcGp04o6qjnkPpDeRrZRPd9zXQgI7fhEJxwuOOsGIjg0bkwGO0cH9JsBlNZTVvK8ddA4bFRpYCvYzmz5CGr-Sn8c6bxHwt7h2oyQL35LKlh2FROn5kHnl-xe1c6VeswzZRQYtBi4qorpJDOrWHjMagobwL8KThaAEO4YAIPq8n2fcAt3_kasI5FXjDI/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. 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