Hi Lorenzo
Doug is the person to answer most of these questions, but yes, you want to sample your raw fMRI data onto the surface, then analyze there so you can take advantage of things like surface-based smoothing. There is no need for an "inverse matrix" to transform back, just the output of bbregister to do the sampling in the first place. You can write the sampled fMRI data into nifti "volumes" that are actually nvertices x ntimepoints arrays.
cheers Bruce
p.s. Thomas Yeo has a very nice analysis stream for surface-based fcMRI, so he may comment as well.
On Thu, 4 Sep 2014, lorenzo pasquini wrote:
Dear Bruce, thank you very much for the quick reply. The aim of our study is to investigate the correspondence of cortical thickness and measures of functional connectivity (e.g. from ICA) on a vertex-based within-subject level. However, we are not sure how to implement this in freesurfer, initially we tried to sample our functional connectivity maps into vertex space without much success. If I understood it correctly, the right strategy would be to to sample the raw fMRI data into vertex space (using nifti format), then perform our functional connectivity analysis on the resampled data, use the inverse normalization matrices to back-reconstruct our functional maps into vertex space, finally investigate the relationship, right? Some practical questions: the output of bbregister and mri_vol2surf is still in nifti format? are this steps building new images or overwrithing the old ones? Can we transform the cortical surface (bearing vertex-based information of cortical thickness) into nifti format? Thank you again for your help! Sincerely,
Lorenzo
Il Mercoledì 3 Settembre 2014 18:18, Bruce Fischl fischl@nmr.mgh.harvard.edu ha scritto:
Hi Lorenzo
we need more information if we are going to be able to help you. What is not working? You should be able to use bbregister on the fMRI data to register it to the surface, then mri_vol2surf to sample it onto the vertex mesh.
Note that you should avoid .img format! Use nifti instead - analyze doesn't have enough information to reliabily distinguish left from right.
cheers Bruce On Wed, 3 Sep 2014, lorenzo pasquini wrote:
Dear Freesurfer users,
I was wondering if it is possible to transform functional connectivity images (.img format) derived e.g. from an ICA of resting state fMRI data into vertex space reflecting cortical thickness (derived from the
Freesurfer
pipeline on anatomical data). We have been trying hard with commands as mrivol2surface and bbregister without much success. Do you have any suggestions why it is not working? Can a correspondence of activity and structure be implemented in Freesurfer only if the activation maps are derived from the freesurfer pipeline? Any help is welcome! Cheers,
Lorenzo
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