| Deletions are marked like this. | Additions are marked like this. |
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| mri_info - provides information about the volume | mri_coreg |
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| mri_info provides information about the volume including voxel size, width, height, depth, direction cosines, etc | This is a program that preforms a linear registration between two volumes in a way that should more-or-less replicate spm_coreg as called by the !FreeSurfer program spmregister. |
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| mri_info fname1 <fname2> <options> | mri_coreg [options] |
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== Positional Arguments == || involume || input volume || |
== Optional Flagged Arguments == |
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== Optional Flagged Arguments == ||-conformed || Print whether a volume is conformed stdout || ||--type || Print the voxel type/precision (e.g. FLOAT) to stdout || ||--tr || Print TR to stdout || ||--te || Print TE to stdout || ||--ti || Print TI to stdout || ||--fa || Print flip angle to stdout || ||--pedir || Print phase encode direction || ||--res || Print col, row, slice, and frame resolution || ||--cres || Print column voxel size (xsize) || ||--rres || Print row voxel size (ysize) || ||--sres || Print slice voxel size (zsize) || ||--voxvol || Print voxel volume || ||--ncols || Print number of columns (width) to stdout || ||--nrows || Print number of rows (height) to stdout || ||--nslices || Print number of slices (depth) to stdout || ||--dim || Print number of columns, rows, slices, and frames || ||--cdc || Print column direction cosine (x_{r,a,s}) || ||--rdc || Print row direction cosine (y_{r,a,s}) || ||--sdc || Print slice direction cosine (z_{r,a,s}) || ||--vox2ras || Print the native/qform vox2ras matrix || ||--ras2vox || Print the native/qform ras2vox matrix || ||--vox2ras-tkr || Print the tkregister vox2ras matrix || ||--ras2vox-tkr || Print the tkregister raz2vox matrix || ||--vox2rax-fsl || Print the FSL/FLIRT vox2ras matrix || ||--tkr2scanner || Print tkrRAS-to-scannerRAS matrix || ||--scanner2tkr || Print scannerRAS-to-tkrRAS matrix || ||--ras_good || Print ras_good_flag || ||--cras || Print the RAS at the center of the volume || ||--zero-cras || Zero the center ras || ||--p0 || Print the RAS at voxel (0,0,0) || ||--det || Print the determinant of the vox2ras matrix || ||--dof || Print the dof stored in the header || ||--nframes || Print number of frames to stdout || ||--mid-frame || Print number of middle frames to stdout || ||--format || File format || ||--orientation || Orientation string (eg. LPS, RAS, RPI) || ||--slicedirection || Primary slice direction || ||--autoalign || Print auto align matrix (if it exists) || ||--cmds || Print command-line provenance info || ||--dump || Print FA, TR, TE, TI, ect || ||--voxel c r s || Dump voxel value from col row slice (0-based, all frames) || ||--entropy || Compute and print entropy || ||--o file || Print flagged results to file || ||--in_type type || Explicitly specify file type (see mri_convert) || = Outputs = || ascii text || description of the volume || |
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{{{ mri_info orig.mgz }}} {{{ Volume information for orig type: COR dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = 5.3997 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.0000 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 0.0000 voxel to ras transform: -1.0000 0.0000 -0.0000 133.3997 -0.0000 0.0000 1.0000 -110.0000 -0.0000 -1.0000 -0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 }}} This is the typical CORONAL volume output. |
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| For more information about the voxel to ras transform (vox2ras), as well as calculating this from scanner raw data, see also [[http://www.nmr.mgh.harvard.edu/~rudolph/software/vox2ras/doc/vox2ras.pdf|this technical report]]. | |
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= Author/s = YasunariTosa |
Index
Contents
Name
mri_coreg
Description
This is a program that preforms a linear registration between two volumes in a way that should more-or-less replicate spm_coreg as called by the FreeSurfer program spmregister.
Synopsis
mri_coreg [options]
Arguments
Optional Flagged Arguments
Examples
Bugs
None
See Also
Links
References
None
Reporting Bugs
Report bugs to <freesurfer@nmr.mgh.harvard.edu>