On 08/20/2016 01:21 PM, Chris Filo Gorgolewski wrote:
Dear FreeSurfer community, I am one of the developers of NeuroVault.org http://NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
- In NeuroVault users are asked to upload their statistical maps in
form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
Yes. You may also want the gamma.mgh file as that is the size of the effect (eg, thickness change in mm )
- I want to be able to tell if a given map is in fsaverage space. Is
there any place in the .mgh header that specifies which space the map is in?
No.
- fsaverage has different subsampling flavours - how often are they
used? Is support for them an important feature?
Not very often. I would probably not worry about it.
- Results come in two files - one per each hemisphere. Is there any
way (from the headers) to check if two files provided by a user match?
match in what way? There is nothing in the mgh file to indicate laterality.
- As with the volumetric data I want to provide a 3D interactive
viewer. I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
I'm not, but I'm not the best person to ask.
- Which surface should be the default view: inflated, pial, or white?
I always to with pial with the aparc outlines. Others may feel differently.
- Finally NeuroVault gives users ability to compare maps and even
search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
I would probably go the other direction, ie, sample the MNI152 maps into surface space.
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer