## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting <> '''Index''' <> = 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 || 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|| || --rot Ax Ay Az || rotation angles (deg) to apply to reg matrix|| || --trans Tx Ty Tz || translation (mm) to apply to reg matrix || || --shear Sxy Sxz Syz || xz is in-plane || || --reg-final regfinal.dat || final reg after rot and trans (but not inv) || || --synth || replace input with white Gaussian noise || || --seed seed || seed for synth (default is to set from time of day) || || --save-reg || write out output volume registration 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 == If a functional volume is f.bhdr (or f.nii.gz, or f.mgh, etc), and the subject is bert, and the registration file is register.dat, then running the following command should show that they are in registration: {{{ tkregister2 --reg register.dat --mov f.nii.gz }}} If they are not, then fix it because nothing below is going to work. You can also check the registration with: {{{ tkmedit bert orig.mgz -overlay f.nii.gz -overlay-reg register.dat }}} The register.dat will look something like this: {{{ bert 3.125 5.000 0.150000 1.000000e+00 0.000000e+00 0.000000e+00 -2.252487e+00 0.000000e+00 -8.902127e-01 4.555448e-01 2.342102e+00 0.000000e+00 4.555449e-01 8.902128e-01 -2.159538e-01 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round }}} '''A.''' To resample the functional into anatomical space: {{{ mri_vol2vol --reg register.dat --mov f.nii.gz --fstarg --o f-in-anat.mgh }}} f-in-anat.mgh will have the same size and geometry as bert/mri/orig.mgz. You can test the result in two ways: * This will show the low-res functional alighned with its resampled self: {{{ tkregister2 --reg register.dat --mov f.nii.gz --targ f-in-anat.mgh }}} * This will show the resampled functional aligned with the anatomical: {{{ tkregister2 --mov f-in-anat.mgh --targ $SUBJECTS_DIR/bert/mri/orig.mgz \ --regheader --reg /tmp/reg }}} '''B.''' To resample the anatomical into the functional space. This is basically the same command line as 1.A, but --inv has been included and the name of the output is changed. {{{ mri_vol2vol --reg register.dat --mov f.nii.gz --fstarg --o anat-in-func.mgh --inv }}} anat-in-func.mgh will be the same size and geometry as f.nii.gz. You can test the result in two ways: * This will show the low-res anat aligned with its hires self: {{{ tkregister2 --reg register.dat --mov anat-in-func.mgh }}} * This will show the resampled anat aligned with the functional: {{{ tkregister2 --mov anat-in-func.mgh --targ f.nii.gz --regheader --reg /tmp/reg }}} '''C.''' Map functional to anatomical without resampling. Rather, change the vox2ras (sform/qform) matrix. This is the same cmd line as 1.A, but --no-resample as been added. {{{ mri_vol2vol --reg register.dat --mov f.nii.gz --fstarg --o f.new.vox2ras.nii.gz --no-resample }}} f.new.vox2ras.nii.gz will have the same dimension and voxel size as f.nii.gz, but its vox2ras (sform/qform) matrix will have changed. You can check the registration in two ways: * The registration is created implicitly from the vox2ras matrix (that is what --regheader does). There's no need to specify and input registration {{{ tkregister2 --mov f.new.vox2ras.nii.gz --s bert --regheader --reg /tmp/reg }}} * Display the functional as an overlay in tkmedit (no registration needed). {{{ tkmedit bert orig.mgz -overlay f.new.vox2ras.nii.gz }}} '''D.''' Map a binary mask in functional space to anatomical space. This is basically the same cmd line as 1.A, but --interp nearest has been added so that it does not try to interpolate the mask (ie, it will still be binary after resampling): {{{ mri_vol2vol --reg register.dat --mov mask.nii.gz --fstarg --o mask-in-anat.mgh --interp nearest }}} == Example 2 == '''A.''' Map functional to talairach (MNI305) space with 2mm isotropic resolution. This is very similar to 1.A with the addition of --tal and --talres 2. {{{ mri_vol2vol --mov f.nii.gz --reg register.dat --o f-in-tal.2mm.mgh --tal --talres 2 }}} f-in-tal.2mm.mgh will be 2mm isotropic with the same geometry as $FREESURFER_HOME/average/mni305.cor.subfov2.mgz. This command will also create f-in-tal.2mm.mgh.reg, which will register the volume with any average MNI305 !FreeSurfer subject (fsaverage is used by default). The resampling can be checked with: * This will show the functional with the fsaverage anatomical: {{{ tkregister2 --mov f-in-tal.2mm.mgh --reg f-in-tal.2mm.mgh.reg }}} '''B.''' Map functional to talairach (MNI305) space with 1mm isotropic resolution. Same as 2.A but use --talres 1. {{{ mri_vol2vol --mov f.nii.gz --reg register.dat --o f-in-tal.1mm.mgh --tal --talres 1 }}} f-in-tal.1mm.mgh will take up 8 times as much space as f-in-tal.2mm.mgh == Example 3 == Apply an MNI transform to data by resampling the anatomical orig.mgz into talairach space using bert/mri/transforms/talairach.xfm: First, check that the talairach.xfm is correct (this is basically the samething as 'tkregister2 --s bert --fstal' in Example 2): {{{ cd bert/mri tkregister2 --targ orig.mgz \ --mov $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm --reg /tmp/reg }}} Now resample: {{{ mri_vol2vol --mov orig.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm \ --o orig-in-mni305.mgz }}} Now test the resampling: {{{ tkregister2 --mov orig-in-mni305.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --reg /tmp/reg --regheader }}} = Bugs = sinc interpolation is broken except for maybe COR to COR. = See Also = [[mri_convert]] [[tkregister2]] = Links = FreeSurfer, FsFast = Methods Description = = References = = Reporting Bugs = Report bugs to = Author/s =