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
- Then place cursor with left button, record with right button
- After 5–6 points, save tags
- Choose transform type to be 7 dof
- 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