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||--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) ||

Index

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

--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

Examples

mri orig

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 this technical report.

Links

FreeSurfer

Methods Description

N/A

References

None

Reporting Bugs

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

Author/s

YasunariTosa

mri_info (last edited 2017-11-28 17:18:10 by MorganFogarty)