Posn

<Argname>

Description

1

<surf_fname>

Input: Surface to register, often {hemi}.sphere

2

<target>

Input: The data to register to. In normal recon-all usage, this is a template file for average surface. Alternatively could also be a single-subject's surface -- see argument '-1' (one), which is useful during the template-development process.

3

<out_fname>

Output surface file to capture registration. Example: {hemi}.sphere.reg

-flag1 ??

brief description

-flag2 ??

brief description

Category

Flag

<Args>

Description

Input

-1

(One) Treats target argument as the name of as a single subject's surface not a template file. (What pattern of filename is required?)

Input

-addframe

<which_field, where_in_atlas (ints)>

Add field which_field with location where_in_atlas in the atlas

Input

-annot

<annot_name>

Zeroes medial wall using annotation {annot_name}

Input

-C

<curvature_fname>

Input

-canon

<canon_name>

Use surface {canon_name} for canonical properties

Input

-inflated

Use inflated surface for initial alignment

Input

-infname

<name>

Uses {name} for inflated surface, for initial alignment. Sets inflated_name, surface_name and curvature_names[0]

Input

-L

<labelfile atlas_gcsa_file label_name>

Specify a manual label to align with atlas label <label name>

Input

-O

<orig_name>

Use {orig_name} for original properties

Input

-overlay

<overlay_file navgs(int)>

Adds a variable to the atlas from {overlay_file}, smoothing it {navgs} times. {subject}/labels/{hemi}.{overlay_file}

Input

-overlay-dir

<overlay_dir>

Changes overlay path: {subject}/{overlay_dir}/{hemi}.{overlay_file}

Input

-sreg

<starting_reg_fname>

Start registration with coordinates in file starting_reg_fname

Output

-jacobian

<jacobian_fname>

Write out jacobian of mapping to file jacobian_fname

Algorithm

-A

<n_averages (int)>

Algorithm

-adaptive

Use adaptive time step integration

Algorithm

-area

<l_area (float)>

Sets l_area

Algorithm

-corr

<l_corr (float)>

Algorithm

-curv

Use smoothwm curvature for final alignment

Algorithm

-dist

<l_dist (float)>

Specify distance term. Sets l_dist and also use_defaults = 0

Algorithm

-dt

<dt (float)>

Sets momentum with dt

Algorithm

-dt_dec

<dt_decrease (float)>

Algorithm

-dt_inc

<dt_increase (float)>

Algorithm

-E

<l_external (float)>

Algorithm

-error_ratio

<error_ratio (float)>

Algorithm

-init

Use initial registration

Algorithm

-lap

<lap (float)>

l_laplacian

Algorithm

-lm

Integrate using line minimization

Algorithm

-M

<momentum (float)>

Chooses integration_type = INTEGRATE_MOMENTUM and sets momentum value

Algorithm

-max_degrees

<max_degrees (float)>

Set max angle for search to max_degrees

Algorithm

-median

Uses median normalization (instead of mean).

Algorithm

-min_degrees

<min_degrees (float)>

Set min angle for search to min_degrees

Algorithm

-multi_scale

<multi_scale (int)>

Use multi_scale scales for morphing

Algorithm

-N

<niterations (int)>

Algorithm

-nangles

<nangles (int)>

Set # of angles/search per scale to nangles

Algorithm

-nbrs

<nbrs (int)>

Use neighborhood size=nbrs

Algorithm

-nlarea

<l_nlarea (float)>

Sets l_nlarea

Algorithm

-nocurv

Do not use smoothwm curvature for final alignment

Algorithm

-nonorm

Disables normalization

Algorithm

-norot

Disables initial rigid alignment

Algorithm

-nosulc

Disables initial sulc alignment

Algorithm

-nsurfaces

<nsurfaces>

Use nsurfaces surfaces/curvatures for alignment

Algorithm

-ocorr

<l_ocorr (float)>

Sets overlay correlation coefficient to l_ocorr

Algorithm

-P

<max_passes (int)>

Limit unfolding to {max_passes} passes

Algorithm

-parea

<l_parea (float)>

Sets l_parea

Algorithm

-remove_negative

<remove_negative (int)>

Non-zero to remove negative triangles with iterative smoothing, or 0 to skip that

Algorithm

-reverse

Mirror image reverse brain before morphing

Algorithm

-rotate

<dalpha, dbeta, dgamma (floats)>

Rotates brain by dalpha, dbeta, dgamma

Algorithm

-S

<scale (float)>

Scales distances by {scale}

Algorithm

-search

Integrating with binary search line minimization

Algorithm

-spring

<l_spring (float)>

Algorithm

-tol

<tol (float)>

Tolerance?

Algorithm

-topology

Preserves the topology of positive area triangles

Algorithm

-vnum, -distances

<nbhd_size, max_nbrs (floats)>

Sets neighborhood parameters

Algorithm

-vsmooth

Use space/time varying smoothness weighting

Algorithm

-W

<write_iterations (int)>

Also triggers diagnostics

Utility

-?, -H, -U

print_help()

Utility

--help

print_help

Utility

-V

<Gdiag_no (int)>

Supplies a vertex number for diagnostics

Utility

-vector

Prints some help for Multiframe mode including listing field names/numbers

Utility

--version

print_version()

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