minc meeting 2003 a short tour of the minc toolset steve robbins

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MINC meeting 2003 A Short Tour of the MINC Toolset Steve Robbins <[email protected]>

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Post on 31-Dec-2015




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  • MINC meeting 2003A Short Tour of the MINC ToolsetSteve Robbins

  • MINC-aware ProgramsVisualization: - Display - register - jiv

    Command-line Tools

  • OutlineInside a MINC fileExample toolsinformationresampingreshapingarbitrary mathGetting more info

  • Inside a MINC FileImage datan-dimensional arrayreal-valuedsometimes interpreted as labelse.g. 0=background, 1=CSF, 2=Gray, 3=WhiteShape of image arrayorder of array axeslength of array along each axisLocation of image array in world space

  • mincinfomincinfo mri_001.mncinput: file mri_001.mncoutput (text on terminal):> mincinfo mri_001.mncfile: mri_001.mncimage: signed__ short 0 to 4095image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 181 1 -72 yspace 217 1 -126 xspace 181 1 -90

  • mincstatsmincstats mri_001.mncinput: file mri_001.mncoutput: text on terminal, histogram file> mincstats mri_001.mnc ...Volume (mm3): 7109137Min: 0Max: 1115712.374Sum: 1.221982704e+12Sum^2: 4.347383143e+17Mean: 171889.0357Variance: 3.160621567e+10Stddev: 177781.3704 ...

  • mincresample: Change Sampling Gridmincresample -like template.mnc mri_001.mnc res_001.mncinput: mri_001.mnc, template.mncoutput: res_001.mncmri_001.mnctemplate.mnc

  • mincresample: interpolationtrilineardefault, fasttricubicsmoother, slowernearest_neighbouruseful for label volumes

  • mincresample: Spatial TransformationT describes transformation from scanner (native) space to standard spacestandard space could be Talairach, MNI_305, ...Tnativestandard

  • mincresample: Spatial Transformationmincresample -transformation T.xfm -like template.mnc mri_001.mnc res_001.mncinput: mri_001.mnc, T.xfm (T_grid_0.mnc), template.mncoutput: res_001.mnc

  • mincreshape: change image arrayextract a sub-block (hyperslab)extract 2D slice of 3D fileextract 3D time point of 4D (x,y,z,t) fileenlarge by zero-paddinguseful with label file created using Display

  • mincreshape (2)re-order dimensionse.g. transverse to coronalno interpolation: new grid coincident with oldunlike mincresample

  • mincaverage (1)mincaverage mri_*.mnc average.mncinput: mri_*.mnc files (all of same shape!)output: average.mncoptionally normalize intensity before averaging

  • mincaverage (2)mincaverage -binarize -binvalue 2 seg_*.mnc gray_prob.mnceach input is binarizedresult at each voxel: probability of gray matter

  • mincmath: Simple Mathmincmath -sub mri_001.mnc mri_002.mnc diff.mncinput: mri_001.mnc, mri_002.mncoutput: diff.mnc

  • minccalc: Complex Mathminccalc -expr 'A[0] == 3 && A[1] != 3' seg_001.mnc seg_002.mnc discrep.mncinput: seg_001.mnc, seg_002.mncoutput: discrep.mncrich set of operationsexpression may contain multiple statementsany number of input filesmultiple output files

  • Common Optionsclobberoverwrite existing filequiet, verbose, debugdefault is -verboseimage storagebyte, short, int, etc

  • Getting Helpmincmath -helpterse reminder of optionsman mincmathmanual pageminc-users @ bic.mni.mcgill.cafriendly, helpful humans