CLI reference
=============

The project exposes a small set of user-facing commands. The homepage README
contains the full usage walkthroughs; this page gives a quick command index and
points to the backing Python modules documented in :doc:`../api/cli`.

robreg
------

IRLS-backed robust image-to-image registration for same-contrast or
closely-related contrast pairs.

Example::

   robreg --mov moving.nii.gz --ref fixed.nii.gz --out moving_to_fixed.lta

multireg
--------

Longitudinal multi-timepoint template construction with reusable LTAs for later
template rebuilds.

Examples::

   multireg --mov tp1.mgz tp2.mgz tp3.mgz --template subject_template.mgz \
            --lta tp1.lta tp2.lta tp3.lta --average median
   multireg --mov tp1_orig.mgz tp2_orig.mgz tp3_orig.mgz \
            --template subject_template_orig.mgz \
            --ixforms tp1.lta tp2.lta tp3.lta --noit --average median

coreg
-----

Image-based cross-modal registration when only images are available.

Example::

   coreg --mov moving.nii.gz --ref fixed.nii.gz --out moving_to_fixed.lta --dof 6

bbreg
-----

Boundary-based registration using cortical surfaces or a segmentation-derived
surface pair.

Example::

   bbreg --mov bold.nii.gz --subject_dir /path/to/subject --out bold_to_t1.lta

vol2vol
-------

Apply a linear transform to an image, reslice to a target geometry, or update
the header only without interpolation. The transform argument is optional, so
the command also covers identity reslicing, dtype conversion, and final output
intensity remapping.

Examples::

   vol2vol --mov bold.nii.gz --transform bold_to_t1.lta --ref T1.mgz --out bold_in_t1.nii.gz
   vol2vol --mov aseg.mgz --ref orig.mgz --interp nearest --keep-dtype --out aseg_in_orig.mgz
   vol2vol --mov bold.nii.gz --transform bold_to_t1.lta --header-only --out bold_header_in_t1.nii.gz

mri
---

Image-volume utilities grouped under a single command, analogous to FreeSurfer's
``mri_mask``, ``mri_info``, ``mri_diff``, and ``mri_binarize``.

**mask** — apply a binary mask to a volume::

   mri mask input.nii.gz mask.nii.gz output.nii.gz
   mri mask input.mgz brain_mask.mgz masked.mgz -T 0.5

**info** — print header and geometry information::

   mri info T1.mgz
   mri info T1.mgz --dim --res --orientation

**diff** — compare two volumes and exit nonzero when they differ::

   mri diff vol1.mgz vol2.mgz
   mri diff vol1.mgz vol2.mgz --thresh 1e-4 --count
   mri diff tp1.mgz tp2.mgz --skip-geo --skip-pix --res-thresh 0.000001

**binarize** — binarize by intensity range or matched label values::

   mri binarize --i aseg.mgz --o wm_mask.mgz --match 2 41
   mri binarize --i T1.mgz --o brain_bin.mgz --min 10 --uchar
   mri binarize --i T1.mgz --o bg.mgz --min 10 --inv

lta
---

Utilities for comparing, concatenating, inverting, and converting
FreeSurfer-adjacent linear transform files. The ``convert`` subcommand supports
``.lta``, ``.xfm``, volumetric tkregister ``.dat``/``.reg``, FSL FLIRT
``.mat``/``.fslmat``, ITK/ANTs 3D affine text ``.tfm``, experimental ANTs
``*GenericAffine.mat``, experimental AFNI ``.aff12.1D``, and NiftyReg affine
text matrices.

Examples::

   lta diff reg1.lta reg2.lta
   lta invert in.lta out.lta
   lta concat a_to_b.lta b_to_c.lta a_to_c.lta
   lta convert talairach.xfm talairach.lta --src-img mov.mgz --dst-img ref.mgz
   lta convert bold_to_orig.mat bold_to_orig.lta --src-img bold.nii.gz --dst-img orig.mgz
   lta convert bold_to_orig.txt bold_to_orig.lta --in-format itk --src-img bold.nii.gz --dst-img orig.mgz
   lta convert bold_to_orig0GenericAffine.mat bold_to_orig_from_antsmat.lta
   lta convert bold_to_orig.aff12.1D bold_to_orig_from_afni.lta
   lta convert bold_to_orig.txt bold_to_orig_from_niftyreg.lta --in-format niftyreg


neuroreg-sys_info
-----------------

Print package, dependency, and runtime information useful for debugging
installations and CI environments.

Example::

   neuroreg-sys_info --developer