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 --mov <movvol> --ref <refvol> --reg reg.lta [options]

Arguments

Required Flagged Arguments

--mov movvol	Source volume
--ref refvol	Target volume (can use --targ also)
--reg reg.lta	Output registration (can use --lta too)

Optional Flagged Arguments

--s subject	forces --ref-mask aparc+aseg.mgz
--dof DOF	Default is 6 (also: --6, --9, --12)
--ref-mask refmaskvol	Mask ref with refmaskvol
--no-ref-mask	Do not mask ref (good to undo aparc+aseg.mgz, put AFTER --s)
--mov-mask movmaskvol	Mask ref with movmaskvol
--threads nthreads
--sd SUBJECTS_DIR
--regdat reg.dat
--no-coord-dither	Turn off coordinate dithering
--no-intensity-dither	Turn off intensity dithering
--sep voxsep1 <--sep voxsep2>	Set spatial scales (def is 2 vox and 4 vox)
--trans Tx Ty Tz	Initial translation in mm (implies --no-cras0)
--rot Rx Ry Rz	Initial rotation in deg
--shear Hxy Hxz Hyz	Initial shear
--params outparamfile	Save parameters in this file
--no-cras0	Do not set translation parameters to align centers of mov and ref
--regheader	Same as no-cras0
--nitersmax n	Default is 4
--ftol ftol	Default is 1.000e-07
--linmintol linmintol	Default is 1.000e-03
--sat SatPct	Saturation threshold, default is 9.999+01
--conf-ref	Conform the reference without rescaling (good for gca)
--no-bf	Do not do brute force search
--bf-lim lim	Constrain brute force search to +/- lim
--bf-nsamp nsamples	Number of samples in brute force search
--no-smooth	Do not apply smoothing to either ref or mov
--ref-fwhm fwhm	Apply smoothing to ref
--mov-oob	Count mov voxels that are out-of-bounds as 0
--no-mov-oob	Do not count mov voxels that are out-of-bounds as 0 (default)
--mat2par reg.lta	Extract parameters out of registration
--debug	Turn on debugging
--checkopts	Do not run anything, just check options and exit
--help	Print out information on how to use this program
--version	Print out version and exit

Bugs

None

Links

FreeSurfer

References

None

Reporting Bugs

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

-  ⇤ ← Revision 1 as of 2017-11-29 12:49:18 → 
  Size: 4175
  Editor: MorganFogarty
  Comment:
+   ← Revision 11 as of 2017-12-05 15:58:22 → ⇥
  Size: 2644
  Editor: MorganFogarty
  Comment:
-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 --mov <movvol> --ref <refvol> --reg reg.lta [options]
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-== Positional Arguments ==
|| involume || input volume ||
+== Required Flagged Arguments ==
||--mov movvol || Source volume ||
||--ref refvol || Target volume (can use --targ also) ||
||--reg reg.lta || Output registration (can use --lta too) ||
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+Line 21:
-||-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_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.
+||--s subject || forces --ref-mask aparc+aseg.mgz ||
||--dof DOF || Default is 6 (also: --6, --9, --12) ||
||--ref-mask refmaskvol || Mask ref with refmaskvol ||
||--no-ref-mask || Do not mask ref (good to undo aparc+aseg.mgz, put AFTER --s) ||
||--mov-mask movmaskvol || Mask ref with movmaskvol ||
||--threads nthreads || ||
||--sd SUBJECTS_DIR || ||
||--regdat reg.dat || ||
||--no-coord-dither || Turn off coordinate dithering ||
||--no-intensity-dither || Turn off intensity dithering ||
||--sep voxsep1 <--sep voxsep2> || Set spatial scales (def is 2 vox and 4 vox) ||
||--trans Tx Ty Tz || Initial translation in mm (implies --no-cras0) ||
||--rot Rx Ry Rz || Initial rotation in deg ||
||--shear Hxy Hxz Hyz || Initial shear ||
||--params outparamfile || Save parameters in this file ||
||--no-cras0 || Do not set translation parameters to align centers of mov and ref ||
||--regheader || Same as no-cras0 ||
||--nitersmax n || Default is 4 ||
||--ftol ftol || Default is 1.000e-07 ||
||--linmintol linmintol || Default is 1.000e-03 ||
||--sat !SatPct || Saturation threshold, default is 9.999+01 ||
||--conf-ref || Conform the reference without rescaling (good for gca) ||
||--no-bf || Do not do brute force search ||
||--bf-lim lim || Constrain brute force search to +/- lim ||
||--bf-nsamp nsamples || Number of samples in brute force search ||
||--no-smooth || Do not apply smoothing to either ref or mov ||
||--ref-fwhm fwhm || Apply smoothing to ref ||
||--mov-oob || Count mov voxels that are out-of-bounds as 0 ||
||--no-mov-oob || Do not count mov voxels that are out-of-bounds as 0 (default) ||
||--mat2par reg.lta || Extract parameters out of registration ||
||--debug || Turn on debugging ||
||--checkopts || Do not run anything, just check options and exit ||
||--help || Print out information on how to use this program ||
||--version || Print out version and exit ||
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+Line 58:
-= 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]].
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-= Author/s =
YasunariTosa