Hi FSL experts
I would like to apply MCFLIRT to 2D (later also 3D) images coming from
calcium imaging experiment (i.e., activation of ~100+ neurons) to
correct for motion. The main differences to fMRI are very small
rotational motion and sometimes poor signal to noise ratio. I have
saved my data as nifti with 1mm voxel size. While SPM seems to work
fine even with default parameters, MCFLIRT does not (way too large
"corrections"). I hope some parameter tweaking might help. Could
someone explain what does these two MCFLIRT parameters actually do in
practice:
-scaling (default is 6.0 )
-rotation (specify scaling factor for rotation optimization tolerances)
I didn't find detailed explanation from FSL website.
Thanks in advance.
-Janne Kauttonen
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