--so surface overlay

Path to surface and matching overlay. Specify full path to a surface and full path to the overlay. Multiple --so flags are possible. Eg, to fill both lh and rh or specify one overlay for white and another for pial.

--lta ltafile

Registration file. LTA contains info about the output space. Do not specify if you want the output to be in conformed space (but specify --subject or --ribbon)

--o outfile

Path to output volume.

--subject subject

When not specifying LTA or ribbon. For use when LTA is not used or does not have a subjectname

--ribbon ribbonfile

When no specifying LTA or subject. Specify path to ribbon rather than using ribbon.mgz

--merge vol

Merge with this vol, replacing surface values. Merge the output volume with this volume. ie each voxel that is not assigned a value from the surface inherits its value from the merge volume.

--surfval surfvalpath <fmt>

This is the source of the surface values, and, optionally, the format. If the format is not included, the format will be inferred from the path name. See FORMATS below. A mask can be created instead; see --mkmask

--mkmask

Create a binary (ie, 1/0) mask of all the locations where a surface vertex intersects a volume voxel. This is done instead of mapping surface values to the volume

--hemi hemisphere (lh or rh)

Hemisphere that the source surface values refer to.

--surf surfname

Surface to use as found in surf directory. The actual surface file name will be hemi.surfname. Default is white.

--projfrac fraction

When sampling into the volume, compute the XYZ of the vertex as the XYZ of the vertex on the white/gray boundary projected fraction of the cortical thickness along the surface normal. For example, to place the vertex half way into the cortical sheet, set fraction = 0.5. The fraction can be any number (including negatives).

--fillribbon

Fill the entire ribbon (iterate projfrac from 0 to 1 by .05)

--fill-projfrac start stop delta

Fill the entire ribbon by iterating projfrac from min to max by delta. Note that the volume can be filled 'into' the surface by setting stop < 0, eg, --fill-projfrac -1 0 0.05

--reg volume registration file

Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are samples on the surface of this subject. Cannot be used with --volregidentify

--identify subjid

Use identity matrix for the registration between the surface and the template volume (ie, template volume is the anatomical ref). Must supply subjid (which is usually obtained from the volreg). Cannot be used with --volreg

--template template volume <fmt>

This is the volume that will be used as a template for the output volume in terms of the field-of-view, geometry, and precision. If the format is not included, the format will be inferred from the path name. Not needed with --merge. See FORMATS below.

--fstal res

Sets volreg to $FREESURFER_HOME/average/mni305.cor.subfov$res.reg and template to $FREESURFER_HOME/average/mni305.cor.subfov$res.mgz res can be 1 or 2.

--merge mergevolume

Merge the output volume with this volume. ie, each voxel that is not assigned a value from the surface inherits its value from the merge volume. The merge volume becomes the template volume (ie, --template not needed or used).

--o output volume

Path name of the output volume. If the format is not included, the format will be inferred from the path name. See FORMATS below.

--vtxvol vertex output volume

Path name of the vertex output volume. The vertex volume is the same as the output volume except that the voxel value is the number of the vertex that mapped to that voxel. If no vertex mapped to a voxel, the value is set to -1. This volume is mainly helped for debugging. If the format is not included, the format will be inferred from the path name. See FORMATS below.

<fmt>

explicitly define the file format

the file format can be explicitly defined following the surfvalpath, template, outvol, and vtxvol flags.

--surfval

surfvalpath

This is the source of the surface values, and, optionally, the format. If the format is not included, the format will be inferred from the path name. See FORMATS below. A mask can be created instead; see --mkmask

--hemi

hemisphere (lh or rh)

Hemisphere (lh or rh) that the source surface values refer to.

--volreg

volume registration file

Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of thissubject.

--mkmask

make a mask instead of loading surfval

Create a binary (ie, 1/0) mask of all the locations where a surface vertex intersects a volume voxel. This is done instead of mapping surface values to the volume.

--surf

surfname (default is white)

Surface to use as found in surf directory. The actual surface file name will be hemi.surfname. Default is white.

--projfrac

thickness fraction

When sampling into the volume, compute the XYZ of the vertex as the XYZ of the vertex on the white/gray boundary projected fraction of the cortical thickncess along the surface normal. For example, to place the vertex half way into the cortical sheet, set fraction = 0.5. The fraction can be any number (including negatives).

--template

output like this volume

This is the volume that will be used as a template for the output volume in terms of the field-of-view, geometry, and precision. If the format is not included, the format will be inferred from the path name. See FORMATS below.

--outvol

output volume path id

Path name of the output volume. If the format is not included, the format will be inferred from the path name. See FORMATS below.

--vtxvol

vertex map volume path id

Path name of the vertex output volume. The vertex volume is the the same as the output volume except that the voxel value is the number of the vertex that mapped to that voxel. If no vertex mapped to a voxel, the value is set to -1. This volume is mainly helpful for debugging. If the format is not included, the format will be inferred from the path name. See FORMATS below.

--sd subjectsdir

FreeSurfer subjects' directory

Use subjectsdir as the FreeSurfer subjects' directory. If unspecified, the value of the environment variable SUBJECTS_DIR is used.

--gdiagno number

set diag level

Sets the diagnostic level (only good for debugging).

--version

print version and exit

Print out version string and exit.

--help

hidden secrets of success

Prints out all this information.