Difference between revisions of "Roy"

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= MIMECS Project Page =
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= [[IACL:MIMECS|MIMECS : '''M'''agnetic resonance '''Im'''age '''E'''xample-based '''C'''ontrast '''S'''ynthesis]] =
  
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== Recent MIMECS developments ==
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A C executable is available here,
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The following results are obtained using optimal number of basis vectors.
 
  
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Left to right,top to bottom, (1) original SPGR, (2) original MPRAGE, (3) synthetic MPRAGE(reported in SPIE, using 10-20 basis), (4) synthetic MPRAGE(new updated, using >500 basis and TOADS priors in search regions).
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/home/roy/Programs/pglib/mimecs/mimecs_v6
  
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The usage is:
  
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Subject AS11, using atlas as GO03
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mimecs [options] input_M1_volume atlas_M1_volume atlas_M2_volume output_M2_volume input_TOADS_memberships atlas_TOADS_memberships
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[[Image:As11.png|700px]]
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            -v    :verbose output (default)
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            -C    :Option to choose what and how many TOADS memberships to use
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                    0 -> no membership is used, only intensities, atlas and subject TOADS membership volumes are not required
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                    1 -> choose CSF, GM and WM memberships
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                    2 -> caudate, putamen and thalamus memberships
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                    3 -> CSF,GM,WM,ventricles,caudate,thalamus,putamen memberships
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            -q    :quiet output
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            -P ###:patch size (default=3x3x3)
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            -l #  :lambda, smoothing of the compressed sensing(CS) (0.0-0.5), default 0.01
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            -t #  :noise threshold (default=0.0)
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            -e #  :CS error tolerance (default=0.00001)
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            -N #  :Number of atlas patches to be chosen (100-500), default 200
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            -m #  :Maximum number of iteration for convergence, default 0, 0 implies iteration till convergence by -e option
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            -c #  :Number of cores used (default 2)
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            -p ## :atlas and subject WHITE MATTER peaks (mandatory)
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            Input and atlas files must be NIFTI in FLOAT32 little-endian format
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            output is written as RAW FLOAT32, little endian. TOADS memberships should be 10 object memberships.
  
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If '''-C 0''' is used, input_TOADS_memberships and atlas_TOADS_memberships are not required.
  
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Example usage:
  
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Subject GO03, using atlas as AS11
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./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
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[[Image:Go03.png|700px]]
 
  
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Test subject and atlases are available in
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/home/roy/Programs/pglib/mimecs/
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/home/roy/atlas/mimecs_atlas/
  
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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,
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/home/roy/atlas/cruise-atlas-10obj-toads2008.txt
  
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Outer surface difference on subject AS11 --
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Use '''-C 0''' and '''-c 4''' on stymie/putter to get the fastest result (~10hrs on a 256x256x199 volume).
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[[Image:Outersurfdiff.PNG|600px]]
 
  
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It needs the following libraries, PGCVS, PGVOL, PGUTIL, NLOPT.
  
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All of them are available in
  
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Inner surface difference on subject AS11 --
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/home/roy/Programs/pglib
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[[Image:Innersurfdiff.PNG|600px]]
 
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Mean inner surface absolute difference between SPGR and original MPRAGE = 1.45 voxels
 
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Mean inner surface absolute difference between synthetic and original MPRAGE = 0.74 voxels (It is reported as 1.02 voxels in the SPIE paper).
 

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
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