Deletions are marked like this. | Additions are marked like this. |
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|| --srcsubject srcsubject || source subject || |
|| --mov movvol || input (or output template with --inv) || || --o outvol || output volume || |
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|| --hemi hemisphere || (lh or rh) || required with --regmethod surface|| |
|| --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) || || --regheader || ScannerRAS-to-ScannerRAS matrix = identity || || --mni152reg || target MNI152 space (need FSL installed) || || --s subject || set matrix = identity and use subject for any templates || || --inv || sample from targ to mov || || --tal || 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 || || --noDefM3zPath || 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 || || --inv-morph || 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 || || --slice-reverse || reverse order of slices, update vox2ras || || --slice-bias alpha || apply half-cosine bias field || || --trilin || trilinear interpolation (default)|| || --nearest || nearest neighbor interpolation || || --cubic || 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) || || --keep-precision || set output precision to that of input || || --kernel || save the trilinear interpolation kernel instead || || --no-resample || do not resample, just change vox2ras matrix|| || |
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= Outputs = ||??||??|| |
Index
Contents
Name
mri_vol2vol - Resamples a volume into another field-of-view using varous types of matrices (FreeSurfer, FSL, SPM, and MNI).
Synopsis
mri_vol2vol
Arguments
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) |
--regheader |
ScannerRAS-to-ScannerRAS matrix = identity |
--mni152reg |
target MNI152 space (need FSL installed) |
--s subject |
set matrix = identity and use subject for any templates |
--inv |
sample from targ to mov |
--tal |
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 |
--noDefM3zPath |
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 |
--inv-morph |
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 |
--slice-reverse |
reverse order of slices, update vox2ras |
--slice-bias alpha |
apply half-cosine bias field |
--trilin |
trilinear interpolation (default) |
--nearest |
nearest neighbor interpolation |
--cubic |
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) |
--keep-precision |
set output precision to that of input |
--kernel |
save the trilinear interpolation kernel instead |
--no-resample |
do not resample, just change vox2ras matrix |
||
Description
General
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.
Notes
The data file format can be specified implicitly (through the path name) or explicitly. All formats accepted by mri_convert can be used.
Examples
Example 1
Bugs
sinc interpolation is broken except for maybe COR to COR.
See Also
Links
Methods Description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>