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| = Name mri_info - provides information about the volume including voxel size, width, height, depth, direction cosines, etc |
'''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 |
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| mri_info [volume] | mri_info fname1 <fname2> <options> |
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| = Positional Arguments = [volume] |
= Arguments = == Positional Arguments == || involume || input volume || |
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| = Required Flagged Arguments = None |
== 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) || |
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| = Optional Flagged Arguments = None |
|
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| = Description = description |
= Examples = {{{ mri_info orig.mgz }}} |
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| {{{ 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 |
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| = Examples = == Example 1 == command foo -i f -o out description == Example 2 == command foo -i f -o out -f fvalue description |
}}} This is the typical CORONAL volume output. |
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| ["othercommand1"], ["othercommand2"] | 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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| FreeSurfer, FsFast = Methods Description = {{{ description description }}} |
FreeSurfer |
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| ["References/Lastname###"] | None |
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| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | Report bugs to <freesurfer@nmr.mgh.harvard.edu> |
Index
Contents
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 1.0000This 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
References
None
Reporting Bugs
Report bugs to <freesurfer@nmr.mgh.harvard.edu>