upped dof to 12, adding slides/markdown

Author: bendhouseart

notebooks/logs/petdeface_20250430_140702.log

@@ -0,0 +1,35 @@
+---
+marp: true
+theme: gaia
+_class: lead
+backgroundColor: #fff
+---
+
+![bg left:40% 80%](media/not1wpng)
+
+# **Defacing: No T1w? No Problem!**
+
+---
+
+# This is my second Slide
+
+Add bids tree with missing t1w's
+
+---
+
+# Using templates
+
+Photo of MNI, Martin's T1w, and an Averaged PET image
+
+---
+
+# Show command line usage to enable templating
+
+---
+
+# Show outputs with registration to Templates
+
+---
+
+# Lastly run motion correction on outputs and show differences
+

notebooks/logs/petdeface_20250501_172824.log

@@ -473,6 +473,9 @@ def init_single_subject_wf(
             # rename registration file to something more descriptive than registration.lta
             # we do this here to account for mulitple runs during the same session
             mricoreg = MRICoreg(reference_file=t1w_file)
+            if use_template_anat:
+                mricoreg.inputs.dof = 12
+            
             mricoreg.inputs.out_lta_file = f"{pet_string}{run_id}_desc-pet2anat_pet.lta"
 
             coreg_pet_to_t1w = Node(mricoreg, "coreg_pet_to_t1w")