[Freesurfer] License on fsaverage datasets

hi As part of developing some tools [1] partly on the FreeSurfer ecosystem, we'd like to use the fsaverage5 dataset as a test data. In our workflow that would mean committing those files to our Git repo, pushing to GitHub, testing on Travis CI etc which makes them public in our repo. We have, howe

[Freesurfer] Problem checking out sources

hi I followed the instructions for checking out the sources, by logging in first and then trying to checkout ~/src/fs$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot co -P -r stable5 dev cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand module

[Freesurfer] Deflate surface

Hi I would like to resample the cortical surface on the sphere at a lower resolution, and then deflate the surface to its folded form. Is this something which can be done using the inflated surface that FS generates? Thank you, Marmaduke ___ Freesurf

Re: [Freesurfer] Deflate surface

Hi On 03/04/2016 07:06 PM, Bruce Fischl wrote: > I think there are some tools around for downsampling the surfaces like > mris_decimate. Have you tried any of them? Yes, indeed mris_decimate works well for the downsampling. However, I'd like to recover the cortical parcellation for the downsam

Re: [Freesurfer] Deflate surface

On 03/04/2016 09:10 PM, marmaduke woodman wrote: > However, I'd like to recover the cortical parcellation for the > downsampled surface. I tried to decimate the pial & white surfaces, generate a corresponding thickness file and then mris_sample_parc -ct /opt/freesurfer/FreeSur

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:06 PM, Bruce Fischl wrote: > what are you trying to achieve? A per-subject ~10k vertex pial surface with a corresponding annot. We use it as a spatial domain for simulating neural activity; 150k vertices is too many for this purpose. > It might be easiest to use something like

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:19 PM, Bruce Fischl wrote: > I think you can map it to fsaverage5 then use mri_surf2surf with > -sval-xyz to map the fsaverage5 surface back to each subject This seems to generate a surface with the number of vertices in the subject, (160k) not fsaverage5 (10k), though perhaps I'

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:50 PM, marmaduke woodman wrote: > On 03/04/2016 10:19 PM, Bruce Fischl wrote: >> I think you can map it to fsaverage5 then use mri_surf2surf with >> -sval-xyz to map the fsaverage5 surface back to each subject Sorry for the noise, fwiw, this seems to do the trick:

[Freesurfer] mri_surf2surf dev vs stable

Hi The command mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh --sval-xyz pial --tval pial.tvb --tval-xyz ./tvb/mri/T1.mgz works on dev (mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve), but on stable fails with ERROR: Option ./tvb/mri/T1.mgz unknown Is there a simple wor

Re: [Freesurfer] mri_surf2surf dev vs stable

On 03/06/2016 08:23 PM, marmaduke woodman wrote: > mri_surf2surf ...--tval-xyz ./tvb/mri/T1.mgz just to follow up, it seems --tval-xyz is a flag (no argument) on stable, but on dev takes an argument. So, on stable, just mri_surf2surf ... --tval-xyz will run, but the resulting surface does

[Freesurfer] Embed vol geom in surf file

hi Is it possible to embed a volume geometry in a surface file explicitly? I'm unable to find a mri_ or mris_ command which seems to do this. Is there any workaround via the GUI tools? Thanks, Marmaduke ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] Embed vol geom in surf file

On 03/07/2016 08:34 PM, dgw wrote: > Marmaduke, > > Could you describe what it is you want to do? What do you mean by > volume geometry? What type of information do you want to put on the > surface? I wish to approximate the effect of the --tval-xyz vol argument to mris_surf2surf in the dev ver

[Freesurfer] Slim down FS6

Hi I'm using just the standard structural recon-all pipeline, nothing else. FS6's directory totals just over 9 GiB. Is there a way to slim that down, or is it all required for the structural pipeline? I'm using Docker containers, hence trying to slim down the image size. Thanks, Marmaduke

Re: [Freesurfer] Slim down FS6 (Marmaduke Woodman)

> On 5 Feb 2017, at 19:07, Alex Cohen wrote: > > Have you looked at the modifications for the BIDS App version: > > https://github.com/BIDS-Apps/freesurfer > No, I admittedly didn't Google hard before asking, but this is a great example to work from.