How to register rat brains

From Louis Collins, how to register a 4D PET scan of a rat brain against a structural atlas. This is primarily interesting to people who are using the microPET.

A0016_02–14–2005_v1_Summed_MAP.mnc - 4D rat raclopride data

rat_brain_VOIs.mnc - the atlas

First - use Register to make tag points between atlas and rat:

register rat_brain_VOIs.mnc A0016_02-14-2005_v1_Summed_MAP.mnc

  1. Then place cursor with left button, record with right button
  2. After 5–6 points, save tags
  3. Choose transform type to be 7 dof
  4. Save transform

The registration tool is MinctraccManPage. It computes the transformation that optimizes the choosen objective function (xcorr, mi, diff, zscore, var of ratios).

NOT WORKING:

minctracc -mi -w_translations 0.01 0.01 0.01 -transformation a16-to-voi.xfm -lsq7 \
    A0016_02-14-2005_v1_Summed_MAP.mnc rat_brain_VOIs.mnc \
    a16-to-voi-mi.1.xfm \
    -step 1 1 1 -simplex 1 -center 37 39.4 51.9 \
    -debug

Remap atlas to have intensities like PET data~:

minclookup -discrete -lut '45 56000; 87 61000; 129 45000; 171 51000; 213 59000; 255 85000' \
    rat_brain_VOIs.mnc rat_brain_VOIs_intensity-like-pet.mnc

autocrop -clobber rat_brain_VOIs_intensity-like-pet.mnc rat_brain_VOIs_intensity-like-pet-padded.mnc -isoexpand 20v
mincblur rat_brain_VOIs_intensity-like-pet-padded.mnc rat_brain_VOIs_intensity-like-pet-blured -fwhm 2.1

mincmath -seg -const2 10000 100000000000 \
 rat_brain_VOIs_intensity-like-pet-blured_blur.mnc rat_brain_VOIs_mask.mnc

minctracc -xcorr -w_translations 0.01 0.01 0.01 -transformation a16-to-voi.xfm -lsq7 \
    A0016_02-14-2005_v1_Summed_MAP.mnc rat_brain_VOIs_intensity-like-pet-blured_blur.mnc \
    -model_mask rat_brain_VOIs_mask.mnc \
    a16-to-voi-xcorr.1.xfm \
    -step 1 1 1 -simplex 1 -center 37 39.4 51.9 \
    -debug

minctracc -xcorr -w_translations 0.01 0.01 0.01 -transformation
    a16-to-voi-xcorr.1.xfm -lsq9 \
    A0016_02-14-2005_v1_Summed_MAP.mnc
    rat_brain_VOIs_intensity-like-pet-blured_blur.mnc \
    -model_mask rat_brain_VOIs_mask.mnc \
    a16-to-voi-xcorr.2.xfm \
    -step 0.5 0.5 0.5 -simplex 0.5 -center 37 39.4 51.9 \
    -debug


mincresample A0016_02-14-2005_v1_Summed_MAP.mnc -like rat_brain_VOIs.mnc \
     A016-like-atlas-xcorr.2.mnc -transformation a16-to-voi-xcorr.2.xfm -clob