Assorted notes

How I cropped the female template

IJ.run(imp, "Slice Remover", "first=1 last=78 increment=1");
IJ.run(imp, "Slice Remover", "first=966 last=1024 increment=1");
imp.setRoi(275,120,3250,1550);
IJ.run(imp, "Crop", "");

How I cropped the textured lo-res female template

IJ.run(imp, "Slice Remover", "first=1 last=42 increment=1");
IJ.run(imp, "Slice Remover", "first=215 last=259 increment=1");
imp.setRoi(100,100,800,425);
IJ.run(imp, "Crop", "");

Applying displacement fields with reformatx

• Forward transforms:
  • (transforming moving to reference)

reformatx --floating <moving> -o <output> <reference> <displacement field> <the affine> 

• Inverse transforms:
  • (transforming reference to moving)

reformatx --floating <referece> -o <output> <moving> -i <the affine> <inverse displacement field>

Testing cmtk to displacement field

cmtk2DField works after bug fix to Concatenate. See this test.

A displacement field:

/nrs/saalfeld/john/projects/flyChemStainAtlas/cmtk_test/MakeAverageBrain/Registration/warp/start-1_F-A5_01_warp_m0g80c8e1e-1x26r4.list/defField.tif

$echo "356 287 119" | streamxform -- registration
344.464788 289.786881 113.647421

This is consistent with the values at (356,287,119) in:

dfield-[xyz].nrrd

Relative x-y scalings between templates

• JFRC10 to JRC18 : 1.0
• JFRC13 to JRC18 : 1.0
• FCWB to JRC18 : 0.513
• Tefor to JRC18: 0.973