Hi Alex, analyzing in the anatomical space is going to be very, very costly in terms of space and memory (and I don't really have a way to do it). It is probably better to do it in mni305 space and turn off the masking out of cortex (-no-subcort-mask). You can then run reg-mni305.2mm to create a registration from mni305 2mm space to your subject's anatomical and then go from there.

doug

Alex Kell wrote:

Hi Freesurfers,

I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion correction (these subjects have a lot of between-run motion), and I want to analyze the volumes in each subject's individual space (I'd prefer native functional space, but I am happy to do it in each subject's anatomical space). Do preproc-sess, mkanalysis-sess, or selxavg3-sess have any built-in flags that would automatically align the functional volumes using the 6 rigid parameters generated from bbregister? Or do they have a built-in way to align and to upsample the functional volumes to the subject's anatomical space (not the surface)? I am happy to upsample each run's functional volume to anatomical space with an mri_vol2vol call, and then to estimate my glm with selxavg3-sess on these volumes. But I figure there may be some flags that do this automatically. I've looked through the documentation and I haven't found these flags. Is this possible to do automatically?

Thanks, guys!

Alex

Kanwisher Lab Manager McGovern Institute for Brain Research MIT

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