Hi FSLers,
1) currently I am trying to figure out how to set the seeding and target masks for a group of subjects for DTI connectivity analyses in combination with fMRI activity maps. What is your suggestion for creating the masks when variability of the step should be minimized?
2) In fact if possible I don't want to draw the masks for every single subject by hand in the diffspace. What I think of is creating an interface mask at the grey-white matter boundary adjacent to a fmri motor spot and extract the 100 nearest mask-voxels to this activation peak. Since this activition peak (x,y,z) is in derived in mni standard space (using SPM), I thought to create this interface mask for each ROI in the FSL MNI template. Does this sound reasonable to you? Will FLIRT/FNIRT work to create proper stand2diff transformations for the semi-automated seeding masks?
3) Generally, what are your experiences in creating masks for specific cortical functional areas (like PMd) minimizing the variability and investigator dependency? Is there a tool for automated mask creation targeting specific cortical region? What should I use? What would be the pipeline?
As new to FSL I thank you so much for your comments and suggestions!
Thanks a lot
Kind regards
Robert
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Robert Schulz
University Medical Center Hamburg-Eppendorf
Department of Neurology
Brain Imaging and NeuroStimulation lab (BINS)
Martinistraße 52
D - 20246 Hamburg
email. [log in to unmask]
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