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


= 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>