[Freesurfer] Setting -openmp flag to more than 8

Hi, We are running freesurfer as part of a bigger pipelines with other steps that can be performed in parallel to freesurfer reconstruction. So far we have set the openmp flag to the number of all available cores. However, our experience with ANTs and AFNI which also capitalize on the OpenMP paral

Re: [Freesurfer] Setting -openmp flag to more than 8

Thank you - this is very useful! On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl wrote: > Hi Chris > > we have found an almost linear speed improvement up to 4, then it starts > to fall off, with not much at all after 8. > > cheers > Bruce > > On Tue, 2 May 2017, Chri

[Freesurfer] FreeSurfer is now available on OpenNeuro.org

Dear all, FreeSurfer BIDS App is now available on the OpenNeuro.org platform. This means that you can run recon-all on your datasets (with longitudinal pipeline and study specific template estimation) in the cloud for free (see example results here

[Freesurfer] [job] Program Manager for the Brain Imaging Data Structure project

successful candidate will receive relocation support. More details at https://stanford.taleo.net/careersection/2/jobdetail.ftl?job=76713&lang=en#.WeUP-AdO9j4.email. We will start reviewing applications on the 6th of November. Best regards, Chris Gorgolewski PS Apologies for cross posting - pl

[Freesurfer] Postdoctoral position available in the Poldrack Lab

Apologies for cross-posting. The Poldracklab at Stanford is looking to hire a postdoc with expertise in fMRI data analysis, starting as soon as possible. Our lab is a dynamic and collaborative group that includes basic cognitive neuroscience researchers focused on the study of decision making and

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Hi Dianne, You need to "mount" the using -v the same way input and output directories are mounted. For example: docker run -ti --rm -v /Volumes/Main/Working/BIDS_ TESTING/license.txt:/license.txt:ro -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

wrote: > >> Wonderful...and makes total sense! Thankyou...it is off and running now. >> -Dianne >> >> >> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski < >> krzysztof.gorgolew...@gmail.com> wrote: >> >>> Hi Dianne, >>> >>>

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

appy > to provide other logs if they would be useful for understanding the > problem. > Any insight into why this is happening would be much appreciated. > > Thanks, > > Dianne > > On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski < > krzysztof.gorgolew...@gmail.com&g

[Freesurfer] Learning which data derivatives matter most

External Email - Use Caution Dear all, To learn which neuroimaging data derivatives (intermediate or final analysis outputs) matter most to people conducting analyses and reusing data we have put together a survey: https://goo.gl/forms/5ghpVbiiPHd8BN153 Please take a moment and f

[Freesurfer] 6.0.1 automatic download

External Email - Use Caution Hi, I noticed that https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz is no longer available, but instead there is https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurf

Re: [Freesurfer] 6.0.1 automatic download

a few days ago and we had to restore some things manually (I guess the > original filename was copied). I renamed the tarball back to > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz > > > > best, > > Andrew > > > > > > *From: * on behalf of Chr