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'''Index'''
<<TableOfContents>>


= Name =
mri_surf2vol 

= Synopsis =
mri_surf2vol [flags] [options]

= Arguments =

== Method One Arguments ==
||--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. ||

== Method Two Arguments ==
||--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 --volregidentity ||
||--identity 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. ||

== Arguments for Both Methods ==
||--add const || Add constant value to each non-zero output voxel ||
||--sd subjectsdir || Use subjectsdir as the !FreeSurfer subjects directory. If unspecified, the value of the environment variable SUBJECTS_DIR is used. ||
||--gdiagno number || Sets the diagnostic level (only good for debugging) ||
||--version || Prints out version string and exit ||
||--help || Prints out help 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.

= Example =
{{{
mri_surf2vol --o thickness-in-volume.nii.gz --subject bert \
--so $SUBJECTS_DIR/bert/surf/lh.white $SUBJECTS_DIR/bert/surf/lh.thickness \
--so $SUBJECTS_DIR/bert/surf/rh.white $SUBJECTS_DIR/bert/surf/rh.thickness
}}}
This will create a conformed volume with the thickness.

= Bugs =

If paint format is used, make sure to put ./ in front of the pathname.

= See Also =
[[mri_convert]], [[mri_vol2surf]]

= Links =
FreeSurfer, FsFast

= 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.


= Author/s =
DougGreve