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 Mercoledė 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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