Pádraig Kitterick wrote:
Dear list,
I am trying to use freesurfer to visualise MEG data (minimum norm) overlayed on the cortical surface, both at an individual and group level. I have successfully processed all of the participants MRIs using recon-all, and have decimated the cortical surface (white) to compute the MEG solution. I would be grateful if anyone could help with the following issues I have run into:
- I would like to know how to view the time-varying solution over the
cortex using tksurfer. I have successfully exported the overlay for a single sample to a .w file (using matlab), and then smoothed it (mri_surf2surf) and viewed it on the cortical surface, which works great. But I am aware that .w format only supports a single 'frame' of data. Some previous posts on the list suggest that exporting the data in .mgh format as a nverts x 1 x 1 x nsamples volume would allow visualisation of the timecourse in tksurfer.
My question is: is there a way to only write out the data for the vertices with values (i.e. left after decimation) when using the mgh format, and not a matrix of the total vertices in the original cortex? For example, if the surface has N vertices, and after decimation I have M vertices left, using the .w format I only need to write out data for the M vertices, along with a list of the vertex numbers to place them on the original surface. Can I do this with .mgh? It is difficult to get matlab to write out an mgh file with a 140000x1x1x500 volume!
You can't do this with the mgh format. You can use compressed mgh (mgz), and that will compress all the 0s, but that probably does not take you where you need to be. How are you decimating your data? One way would be to create a decimated average subject with a lower order icosahedron and then use that as the target for mri_surf2surf.
- I wish to view the average data across several subjects, mapped
onto the fsaverage subject template. I have seen that mris_preproc can warp one or more overlays onto a single subject. My question is: will mris_preproc work with the type of .mgh files I described above, i.e. containing multiple frames of data overlay? Or am I better trying to do the whole operation with .w files, with one per timepoint?
You can do it with multiple frame input (though the output frames will be a stack of original frames from all the subjects).
doug
Many thanks in advance,
Padraig