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'''Index'''
<<TableOfContents>>


= Name =
mri_info - provides information about the volume

= Description =
mri_info provides information about the volume including voxel size, width, height, depth, direction cosines, etc

= Synopsis =
mri_info fname1 <fname2> <options>

= Arguments =
== Positional Arguments ==
|| involume || input volume ||

== Optional Flagged Arguments ==
||--conformed || Print whether a volume is conformed stdout ||
||--conformed-to-min || Print whether a volume is conformed-to-min stdout ||
||--is-1mm-iso || Print whether the voxel size is 1mm isotropic ||
||--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 ||
||--voxvolsum || Compute sum of all voxels times the 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 (at nv/2) ||
||--center || Print the RAS at the actual center of the volume (at (nv-1)/2) ||
||--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) ||
||--ctab || Print embedded color lookup table ||
||--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 ||

= Examples =
{{{
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.

= Bugs =
None

= See Also =
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]].

= Links =
FreeSurfer

= References =
None

= Reporting Bugs =
Report bugs to <freesurfer@nmr.mgh.harvard.edu>

= Author/s =
YasunariTosa