freesurfer
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bids-apps
BIDS app wrapping recon-all from FreeSurfer
Hi, I need to skip the automatic failure detection of Talairach alignment for a few subject (-notal-check flag). Perhaps I missed something in the documentation, but I couldn't find a...
### Your idea I have a couple of subjects with several runs of T1w or FLAIR and I naively thought that `.bidsignore` was an (okay) place to indicate which runs...
T2/FLAIR can be input on resumed recon-all, so we want that option. Usecase: - run autorecon1: this without passing T2/FLAIR (otherwise autorecon1 crashes trying to load surfaces not yet produced)...
### What version of the bids app were you using? Version 6 and Version 7 have the same problem. ### Describe your problem in detail. > `docker pull bids/freesurfer:6` >...
Hi gang, I think we should add a `CoC` and `contributor guidelines` to make it easier for new folks to become an active part and ensure community standards. Looking around...
Hi, I have recently been using this container to run FreeSurfer 6.0, using Singularity (v3.8) on an HPC Cluster on a large number of subjects. I was able to run...
Hello together! Some time ago I've created a minimal freesurfer image that is based on freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 and is able to run recon-all. It is only 732.6 MB compressed and 1.93GB...
Thanks to those who are updating this (@Shotgunosine, @PeerHerholz, and anyone I didn't notice). Given that the `openmp` flag is being passed to `recon-all` should this also include `-parallel` (i.e....
hello, After I updated the vertex_label of rh.aparc.a2009s.annot with an algorithm, now I want to replace the vertex_label in the .annot with the updated vertex_label, mainly to see the effect...
