subject

subject in which to look, inside $SUBJECTS_DIR

hemisphere

lh or rh

surface

name of the surface file. Egs: white or pial

Category

Flag

<Args>

Description

Input

-curv

Load ?h.curv

Input

-lrrev

LeftRightRev = TRUE;

Input

-orig

<orig_suffix>

Use supplied orig suffix (default 'orig')

Input

-patch

<patch_name>

Load a patch file.

Input

-sdir

<sdir>

Subject dir (overrides SUBJECTS_DIR envt var)

Input

-sphere

<sphere_reg_suffix>

Uses supplied sphere suffix (default 'sphere')

Input

-white

<white_suffix>

Uses supplied white suffix (default 'white')

Mask

-mask

<mrismaskfile>

Load a mask file containing per-vertex values for a mask. Can be a list of per-vertex values stored in a volume-format file. (Is this feature supported? --GW)

Mask

-mask-thresh

<mrismaskthresh>

File of per-vertex values to which the per-vertex values in mrismaskfile are compared, resulting in each vertex being masked in or out. (...of what? Painting? Coloring? Stats? -- GW)

Labels

-annot or -annotation

<annotation_fname>

Imports an annotation file to provide s a set of labels on the surface.

Labels

-aparc

Shortcut to load annotation aparc.annot:
strncpy (annotation_fname, 'aparc.annot',
sizeof(annotation_fname));
load_annotation = TRUE;
labl_draw_style = LABL_STYLE_OUTLINE;

Labels

-ctab or -colortable

<colortable_fname>

Load a default color table for labels and annotations.

Labels

-labels-under

labels_before_overlay_flag = TRUE;

Color

-colscalebarflag

<colscalebarflag>

1 or 0. Turn on the color bar.

Color

-colscalebarvertflag

<colscalebarvertflag>

1 or 0. Display color scale bar

Color

-colscaletext

<colscalebartextflag>

1 or 0. Display text in color scale bar

Color

-gray

Load ?h.curv and display it in grayscale. (As opposed to painting the surface plain gray, or portraying curv using red-green scale.)

Color

-scalebarflag

<scalebarflag>

1 or 0. Display the scale bar

Display

-delink

Disables the feature where tool window 'docks' below surface-view window. (2008-02-23: Flag accepted but feature broken. Will submit recommended changes --GW).

Display

-offset

<offset>

(float) 'Set the lighting offset value.' (Looks like it controls some aspect of brightness of surface. --GW)

Display

-title

<tkstitle>

Title for image window.

Overlay

-invphaseflag

<invphaseflag>

1 or 0. Invert the phase of the overlay data.

Overlay

-o or -ov or -overlay

<functional_fname>

Loads a file containing fMRI values. Could be either a volume file, or a file containing per-vertex functional data stored in a volume-format file (or possibly even a .w format file).
Also:
load_curv = TRUE;
forcegraycurvatureflag = TRUE;

Overlay

-orf or -ovreg or -overlay-reg

<overlay_reg>

Specify registration file for overlay.

Overlay

-overlay-reg-find

Attempt to find a register.dat file in the same directory as the overlay data.

Overlay

-overlay-reg-identity

Calculate an identity matrix for overlay registration.

Overlay

-ovnew

UseNewOverlay=1 Invokes alternative coloring algorithm. (Not sure the purpose).

Overlay

-revphaseflag

<revphaseflag>

1 or 0. Reverse the phase of the overlay data.

Overlay

-truncphaseflag

<truncphaseflag>

1 or 0. Truncate the overlay data.

Functional

-fmid

<fmid>

(float) Set the functional midpoint value.

Functional

-foffset

<foffset>

(float) For functional, set the offset of the blue value.

Functional

-fslope

<fslope>

(float) Set the functional slope value.

Functional

-fthresh

<fthresh>

(float) Set the functional threshold value.

Functional

-t or -timecourse

<timecourse_fname>

Load a functional time course volume.

Functional

-timecourse-offset

<timecourse_offset_fname>

Loads the offset volume for the functional time course.

Functional

-timecourse-offset-reg-file

<timecourse_reg>

Specify a registration file for the time course offset.

Functional

-timecourse-offset-reg-find

Attempt to find a register.dat file in the same directory as the time course offset data.

Functional

-timecourse-offset-reg-identity

Calculate an identity matrix for time course offset registration.

Functional

-timecourse-reg-find

timecourse_reg_type = FunD_tRegistration_Find;

Functional

-timecourse-reg-identity

timecourse_reg_type = FunD_tRegistration_Identity;

Functional

-treg or -timecourse-reg

<timecourse_reg>

Also: timecourse_reg_type = FunD_tRegistration_File;

Utility

-h or -help

Show Help info

Utility

-reassign

Reassigns label vertex numbers (?)

Utility

-tcl

<script_tcl>

Load and run a tcl script