Index
Contents
Name
mri_surf2vol
Synopsis
mri_surf2vol [flags] [options]
Arguments
Positional Arguments
<fmt> |
explicitly define the file format |
the file format can be explicitly defined following the surfvalpath, template, outvol, and vtxvol flags. |
Required Flagged Arguments
--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. |
Optional Flagged Arguments
--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. |
Outputs
See Formats below.
Formats
Data file format can be specified implicitly (through the path name) or explicitly. All formats accepted by mri_convert can be used. In addition, the surface value file can be paint format. If paint format is used, make sure to put ./ in front of the pathname.
Description
This command resamples a surface into a volume using one of two methods.
Method One
This method fills the ribbon by construction using ribbon.mgz.
Method Two
This method is the option to now not fill the ribbon. The ribbon fill uses projection instead of construction and so this can leave some holes.
Examples
Bugs
If paint format is used, make sure to put ./ in front of the pathname.
See Also
Links
Methods Description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>. Include the following formatted as a list as follows: (1) command-line, (2) directory where the program was run (for those in the MGH-NMR Center), (3) version, (4) text output, (5) description of the problem.