Roy

MIMECS : Magnetic resonance Image Example-based Contrast Synthesis

A C executable is available here,

/home/roy/Programs/pglib/mimecs/mimecs_v6

The usage is:

mimecs [options] input_M1_volume atlas_M1_volume atlas_M2_volume output_M2_volume input_TOADS_memberships atlas_TOADS_memberships
            -v    :verbose output (default)
            -C    :Option to choose what and how many TOADS memberships to use
                   0 -> no membership is used, only intensities, atlas and subject TOADS membership volumes are not required
                   1 -> choose CSF, GM and WM memberships
                   2 -> caudate, putamen and thalamus memberships
                   3 -> CSF,GM,WM,ventricles,caudate,thalamus,putamen memberships
            -q    :quiet output
            -P ###:patch size (default=3x3x3)
            -l #  :lambda, smoothing of the compressed sensing(CS) (0.0-0.5), default 0.01
            -t #  :noise threshold (default=0.0)
            -e #  :CS error tolerance (default=0.00001)
            -N #  :Number of atlas patches to be chosen (100-500), default 200
            -m #  :Maximum number of iteration for convergence, default 0, 0 implies iteration till convergence by -e option
            -c #  :Number of cores used (default 2)
            -p ## :atlas and subject WHITE MATTER peaks (mandatory)
            Input and atlas files must be NIFTI in FLOAT32 little-endian format
            output is written as RAW FLOAT32, little endian. TOADS memberships should be 10 object memberships.

If -C 0 is used, input_TOADS_memberships and atlas_TOADS_memberships are not required.

Example usage:

./mimecs_v6 -C 0 -c 4 -P 3 3 3 -p 1534 1068 as11_spgr.nii go03_spgr.nii go03_mprage.nii as11_spgr_333.raw

Test subject and atlases are available in

/home/roy/Programs/pglib/mimecs/
/home/roy/atlas/mimecs_atlas/

TOADS memberships are obtained from TOADS2008 using full segmentation as the output. It should be a 4D volume having 11 components, as par the following atlas file,

/home/roy/atlas/cruise-atlas-10obj-toads2008.txt

Use -C 0 and -c 4 on stymie/putter to get the fastest result (~10hrs on a 256x256x199 volume).

It needs the following libraries, PGCVS, PGVOL, PGUTIL, NLOPT.

All of them are available in

/home/roy/Programs/pglib