Re: [Freesurfer] Freesurfer V6 beta
Hi Bruce, Is there any new timeline regarding the release of the v6 beta? Because I'm currently waiting on that version for my project's work because of the new hipppocampal module and knowing that will help me a lot. Thanks, Tyson On Tue, May 3, 2016 at 5:51 AM, Bruce Fischl wrote: > Hi Tyson > > we are moving through our testing and hoping to get it out soon. Hard to > say more definitively than that > > sorry > Bruce > > > On Mon, 2 May 2016, Francis Tyson Thomas wrote: > > > Hello Fresurfer admin! > > I was looking for the v6 beta and it looks like it still hasn't been > > released after it was pulled down the last time. I would like to know > what > > is the expected ETA for the beta. Last I remember it was mentioned it was > > on the verge of release about two weeks ago.I'm looking forward to get my > > hands on the beta! > > > > Thanks, > > Tyson > > > > > ___ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer V6 beta
Hi Tyson we are moving through our testing and hoping to get it out soon. Hard to say more definitively than that sorry Bruce On Mon, 2 May 2016, Francis Tyson Thomas wrote: > Hello Fresurfer admin! > I was looking for the v6 beta and it looks like it still hasn't been > released after it was pulled down the last time. I would like to know what > is the expected ETA for the beta. Last I remember it was mentioned it was > on the verge of release about two weeks ago.I'm looking forward to get my > hands on the beta! > > Thanks, > Tyson > > ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer v6 beta
Hi again, in the paper, we used FreeSurfer 5.3 the process the data (recon-all), and then run the hippocampal module on top of that. So, with a bit of trouble, you can reproduce the results.. However, the 6.0 beta was taken down, so reproducing the results of the recon-all stream would be hard, and since such results affect the hippocampal module, reproducing the subfield segmentation would in turn also be hard. Does this make sense? Cheers, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" To: "Freesurfer support list" Sent: Thursday, April 14, 2016 1:04:31 AM Subject: Re: [Freesurfer] Freesurfer v6 beta Hi Eugenio, I understood this part that you mentioned but I didn't understand how is is affected and what would be its consequences? Because I am referring to your preprint paper that makes use of v6, so will the results/validity of that paper also get affected by these differences. Because in my work the accuracy of the segmentation outputs are critical both for analysis and speeding it up. Thanks, Tyson On Wed, Apr 13, 2016 at 3:52 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: Hi Tyson, the hippocampal module shouldn't change between your beta and the FS6 release, but the main recon-all stream will. Since the latter is used to initialize the former, the results will be a bit different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" < francisttho...@email.arizona.edu > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, April 13, 2016 8:19:18 PM Subject: [Freesurfer] Freesurfer v6 beta Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer v6 beta
Hi Eugenio, I understood this part that you mentioned but I didn't understand how is is affected and what would be its consequences? Because I am referring to your preprint paper that makes use of v6, so will the results/validity of that paper also get affected by these differences. Because in my work the accuracy of the segmentation outputs are critical both for analysis and speeding it up. Thanks, Tyson On Wed, Apr 13, 2016 at 3:52 PM, Eugenio Iglesias wrote: > Hi Tyson, > the hippocampal module shouldn't change between your beta and the FS6 > release, but the main recon-all stream will. Since the latter is used to > initialize the former, the results will be a bit different. > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > -- > *From: *"Francis Tyson Thomas" > *To: *"Freesurfer support list" > *Sent: *Wednesday, April 13, 2016 8:19:18 PM > *Subject: *[Freesurfer] Freesurfer v6 beta > > Hi, > > I was wondering when would the new Freesurfer v6 beta be available? Also I > have been using the old beta for my hippocampal segmentation and I wanted > to know if this new beta will affect the results of that? > > Thanks, > Tyson > > ___ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer v6 beta
Hi Tyson, the hippocampal module shouldn't change between your beta and the FS6 release, but the main recon-all stream will. Since the latter is used to initialize the former, the results will be a bit different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" To: "Freesurfer support list" Sent: Wednesday, April 13, 2016 8:19:18 PM Subject: [Freesurfer] Freesurfer v6 beta Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer v6 beta
Indeed the v6.0 beta was removed,,, not because of a "major" bug but rather it was just decided that significant development was still needed before a true beta could be released. We continue to make improvements and will be releasing a v6 beta soon, but at this point if you want the latest version of freesurfer you will need to download the dev (nightly build) version. -Zeke On 03/11/2016 07:22 PM, Francis Tyson Thomas wrote: > Hi folks, > > I was just wondering if there was any major bug in the freesurfer v6 > beta that necessitated the removal of the beta from your servers because > I cannot find them anymore. Does that mean I will have to go with the > dev version at this point which are like the nightlies of the freesurfer > v6 updated every few days. > > Thanks, > Tyson > > > ___ > 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)
For those who do not know, Apple's latest release of OSX 10.11 (El Capitan) implements SIP (https://support.apple.com/en-us/HT204899), a sort of security protection technology, that unfortunately breaks the way freesurfer passes library paths. We are currently making changes to the code so that freesurfer version 6 (when it is released) will be compliant with the new OSX changes. Until that time, you can get freesurfer to run properly on your El Capitan system by temporarily disabling SIP. See the following link for instructions: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ Hope this helps. -Zeke > Dear all, > > I was wondering if many users have had freesurfer 6 (beta) working (well) > with Mac OS 10.11? > > (or Freesurfer V5.3) > > Thanks! > > > *Dr Kevin Aquino* > Research fellow, > Sir Peter Mansfield Magnetic Resonance Center, The University of > Nottingham. > > Honorary Research Fellow > School of Physics, Faculty of Science, University of Sydney > > *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W* > www.physics.usyd.edu.au/~aquino/ > > -- > > The brain is a wonderful organ. It starts working the moment you get up > and > does not stop until you get into the office. > - > Robert Frost > > CRICOS 00026A > This email plus any attachments to it are confidential. Any unauthorised > use is strictly prohibited. If you receive this email in error, please > delete it and any attachments. > > Please think of our environment and only print this e-mail if necessary. > ___ > 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.