Hi Finn, this is much easier to handle in 5.1. Just put all the runs in the same bold directory and everything should work properly.

doug

Finnegan Calabro wrote:

Hi all, we have a subject who had to end a run early, and as a result his data is split over two sessions. The two sessions can't be analyzed independently, since some events are missing from each, which causes selxavg3 to fail. Instead, what I've been trying to do is take the timecourses of the individual sessions and map them into a common space, and then re-run the functional analysis. Basically:

• make_average_subject to get an averaged brain between the two runs
• convert each fmcsm5.nii timecourse to this averaged brain
• run selxavg3-sess on the combined data in the averaged brain space

The averaged brain looks fine, but I'm running into problems on the second step. I've been trying to use mri_vol2vol for this, but I'm not entirely sure what to use for the target (if I use the T1 of the averaged brain, it'll be up-sampled into anatomical space, right? But I don't have anything else associated with the averaged brain to use).

Does anyone know whether this is a reasonable approach for dealing with the situation? And if so, what should the mri_vol2vol command look like in step 2?

This is still being done in freesurfer 4.5 for compatibility, but moving to 5.1 isn't out of the question if this has become easier to handle.

Thanks! Finn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer