Difference between revisions of "Roy"
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− | = MIMECS | + | = [[IACL:MIMECS|MIMECS : '''M'''agnetic resonance '''Im'''age '''E'''xample-based '''C'''ontrast '''S'''ynthesis]] = |
− | + | 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 |
Latest revision as of 17:46, 21 December 2011
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