mri_vol2vol - Resamples a volume into another field-of-view using varous types of matrices (FreeSurfer, FSL, SPM, and MNI).




Required Flagged Arguments

--mov movvol

input (or output template with --inv)

--o outvol

output volume

Optional Flagged Arguments

--targ targvol

output template (or input with --inv)

--disp dispvol

displacement volume

--reg register.dat

tkRAS-to-tkRAS matrix (tkregister2 format)

--lta register.lta

Linear Transform Array (usually only 1 transform)

--fsl register.fsl

fslRAS-to-fslRAS matrix (FSL format)

--xfm register.xfm

ScannerRAS-to-ScannerRAS matrix (MNI format)


ScannerRAS-to-ScannerRAS matrix = identity


target MNI152 space (need FSL installed)

--s subject

set matrix = identity and use subject for any templates


sample from targ to mov


map to a sub FOV of MNI305 (with --reg only)

--talres resolution

set voxel size 1mm or 2mm (def is 1)

--talxfm xfmfile

default is talairach.xfm (looks in mri/transforms)

--m3z morph

non-linear morph encoded in the m3z format


flag indicating that the code should not be looking for the non-linear m3z morph in the default location (subj/mri/transforms), but should use the morph name as is


compute and use the inverse of the m3z morph

--fstarg <vol>

optionally use vol from subject in --reg as target. default is orig.mgz

--crop scale

crop and change voxel size

--slice-crop sS eE

crop output slices to be within sS and eE


reverse order of slices, update vox2ras

--slice-bias alpha

apply half-cosine bias field


trilinear interpolation (default)


nearest neighbor interpolation


cubic B-Spline interpolation

--interp interptype

interpolation cubic, trilin, nearest (default is trilin)

--mul mulval

multiply output by mulval

--precision precisionid

output precision (default is float)


set output precision to that of input


save the trilinear interpolation kernel instead


do not resample, just change vox2ras matrix




Resamples a volume into another field-of-view using various types of matrices (FreeSurfer, FSL, SPM, and MNI). This is meant to be used in conjunction with tkregister2.


The data file format can be specified implicitly (through the path name) or explicitly. All formats accepted by mri_convert can be used.


Example 1


sinc interpolation is broken except for maybe COR to COR.

See Also

mri_convert tkregister2


FreeSurfer, FsFast

Methods Description


Reporting Bugs

Report bugs to <>