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Name

mri_vol2surf - assigns values from a volume to each surface vertex

Synopsis

mri_vol2surf [<options>] --src inputfile --out outpufile --srcreg registrationfile --hemi hemisphere

Arguments

Required Flagged Arguments

--src	input volume path
--out	output path
--srcreg registrationfile	source registration file	RegistrationFile as computed by tkregister, tkmedit, mri_make_register, or spmmat2register. The volume is mapped onto the surface of subject subjectname (unless --trgsubject is specified). There may or may not be another line with the method used to convert voxel indices from floating to integer during registration. If tkregiser was used to register the volume, the method should be blank or 'tkregister' (no quotes), otherwise it should be 'round'. This can be overridden with --float2int.
--hemi	hemisphere (lh or rh)

Optional Flagged Arguments

--src_type	input volume fileformat
--float2int	float-to-int conversion method (<round>, tkregister )	override float2int method in registration file. See BUGS.
--fixtkreg	make make registration matrix round-compatible	Attempt to convert the registration matrix so that it is round (or nearest neighbor) compatible. Setting this flag will only have an effect if the float2int method is tkregister. It will 'fix' the matrix and change the float2int method to round. Don't use this flag unless you know what you are doing.
--fwhm FWHM	smooth input volume (mm)	Smooth input volume with a gaussian kernal with FWHM mm.
--trgsubject	target subject (if different than reg)	resample volume onto this subject instead of the one found in the registration file. The target subject can be either a subject name (as found in $SUBJECTS_DIR) or ico (to map onto the sphere). If the target subject is not the source subject, then the surfaces are mapped using each subject's spherical surface registration (?h.sphere.reg or that specified with --surfreg). If the target subject is ico, then the volume is resampled onto an icosahedron, which is used to uniformly sample a sphere. This requires specifying the icosahedron order (see --icoorder).
--surf	target surface (white)	the surface on which to resample. The default is white. It will look for $SUBJECTS_DIR/subjectname/surf/?h.surfacenam

With --trgsubject

--surfreg

intersubjectregsurface

Default=sphere.reg. This is a representation of a subject's cortical surface after it has been registered/morphed with a template spherical surface.

||--icoorder||order of icosahedron when trgsubject=ico|| this specifies the size of the icosahedron according to the following table

Order Number of Vertices
- 0 12 1 42 2 162 3 642 4 2562 5 10242 6 40962 7 163842

In general, it is best to use the largest size available.

Surface Normal Proection

--projfrac frac	(0->1)fractional projection along normal
--projdist mmdist	distance projection along normal

Output

--out_type	output format
--frame	save only nth frame (with paint format)
--noreshape	do not save output as multiple 'slices'
--rf R	integer reshaping factor, save as R 'slices'
--srchit	volume to store the number of hits at each vox
--srchit_type	source hit volume format
--nvox nvoxfile	write number of voxels intersecting surface

Other

--srcsynth seed	synthesize source volume
--seedfile fname	save synth seed to fname
--help	print out information on how to use this program
--version	print out version and exit

Outputs

??	description
??	description

Description

SPECIFYING THE INPUT/OUTPUT PATH and TYPE

mri_vol2surf accepts all input/output types as mri_convert (see mri_convert --help for more information). In addition, an output type of 'paint' can be specified. This outputs data in a form that can be easily read by tksurfer (also known as a '.w file'). See BUGS for more information on paint output.

NOTES

The output will be a data set with Nv/R colums, 1 row, R slices, and Nf frames, where Nv is the number of verticies in the output surface, and Nf is the number of frames in the input volume (unless the output format is paint, in which case only one frame is written out). R is the reshaping factor. R is 6 for the icosaheron. For non-ico, the prime factor of Nv closest to 6 is chosen. Reshaping can be important for logistical reasons (eg, Nv can easily exceed the maximum number of elements allowed in the analyze format). R can be forced to 1 with --noreshape. The user can also explicity set R from the command-line using --rf. Any geometry information saved with the output file will be bogus. When resampling for fixed-effects intersubject averaging, make sure to resample variance and not standard deviation. This is automatically accomplished when the input volume has been produced by ["selxavg-sess"].

Examples

Example 1

To paint the third frame of bfloat volume sig registered with tkregister onto a the left hemisphere of a surface

mri_vol2surf --src sig --src_type bfloat --srcreg register.dat --hemi lh --o ./sig-lh.w --out_type paint --float2int tkregister --frame 2

This will create sig-lh.w in the current directory, which can then be loaded into tksurfer

Example 2

To convert an analyze volume onto the sphere (right hemisphere)

mri_vol2surf --src sig.img --src_type analyze --srcreg register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int round --trgsubject ico --icoorder 7

Bugs

When the output format is paint, the output file must be specified with a partial path (eg, ./data-lh.w) or else the output will be written into the subject's anatomical directory.

Currently no support for searching along the surface normal for a maximum value (as can be done with the paint program)

The ability to put the float2int conversion method in the registration file is new as of Fall 2001. Consequently, there may be some registration files that do not have a method string, which will force the method to be that of tkregister. This is can be overridden with --float2int.

Links

FreeSurfer, FsFast

Methods Description

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References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

DougGreve