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| mri_label2label - converts a label in one subject's space to a label in another subject's space using either Talairach space or spherical space as an intermediate registration space | mri_vol2vol - Resamples a volume into another field-of-view using varous types of matrices (!FreeSurfer, FSL, SPM, and MNI). |
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| mri_label2label [<options>] --srcsubject srcsubject --srclabel srclabelfile --trgsubject trgsubject --trglabel trglabelfile --regmethod registrationmethod <<BR>> mri_label2label [<options>] --srcsubject srcsubject --srclabel srclabelfile --trgsubject trgsubject --trglabel trglabelfile --regmethod surface --hemi hemisphere |
mri_vol2vol |
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| || --srcsubject srcsubject || source subject || || --srclabel srclabelfile || input label file || || --trgsubject trgsubject || target subject || || --trglabel trglabel || output label file] || || --regmethod registrationmethod || Legal values: surface, volume || |
|| --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|| || --srchemi hemisphere || (lh or rh) (with surface) || || --trghemi hemisphere || (lh or rh) (with surface) || || --srcicoorder n || when srcsubject=ico || || --trgicoorder n || when trgsubject=ico|| || --trgsurf || get xyz from this surface (white) || || --surfreg srfregfile || surface registration (sphere.reg)] || || --srcsurfreg srcsurfregfile || source surface registration (sphere.reg) || || --trgsurfreg trgsurfregfile || target surface registration (sphere.reg) || || --srcmask surfvalfile || || --srcmasksign sign || Legal values: <abs>, pos, neg || || --srcmaskframe frameno || 0-based frame number. Default = 0. || || --projabs dist || project dist mm along surf normal || || --projfrac frac || project frac of thickness along surf normal || || --sd subjectsdir || Default=SUBJECTS_DIR || || --nohash || don not use hash table when regmethod is surface || || --norevmap || do not use reverse mapping regmethod is 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|| || --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 || |
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| = Outputs = ||??||??|| |
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| Converts a label in one subject's space to a label in another subject's space using either talairach or spherical as an intermediate registration space. If a source mask is used, then the input label must have been created from a surface (ie, the vertex numbers are valid). The format can be anything supported by mri_convert or curv or paint. Vertices in the source label that do not meet threshold in the mask will be removed from the label. See Example 2. | 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. |
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| 1. A label can be converted to/from talairach space by specifying the target/source subject as 'talairach'. 1. A label can be converted to/from the icosahedron by specifying the target/source subject as 'ico'. When the source or target subject is specified as 'ico', then the order of the icosahedron must be specified with --srcicoorder/--trgicoorder. 1. When the surface registration method is used, the xyz coordinates in the target label file are derived from the xyz coordinates from the target subject's white surface. This can be changed using the --trgsurf option. 1. When the volume registration method is used, the xyz coordinates in the target label file are computed as xyzTrg = inv(Ttrg)*Tsrc*xyzSrc where Tsrc is the talairach transform in srcsubject/mri/transforms/talairach.xfm, and where Ttrg is the talairach transform in trgsubject/mri/transforms/talairach.xfm. 1. The registration surfaces are rescaled to a radius of 100 (including the ico) 1. Projections along the surface normal can be either negative or positive, but can only be used with surface registration method. |
The data file format can be specified implicitly (through the path name) or explicitly. All formats accepted by mri_convert can be used. |
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| If you have a label from subject fred called broca-fred.label defined on fred's left hemispherical surface and you want to convert it to sally's surface, then | 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: |
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| mri_label2label --srclabel broca-fred.label --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod surface --hemi lh | tkregister2 --reg register.dat --mov f.nii.gz |
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| This will map from fred to sally using sphere.reg. The registration surface can be changed with --surfreg. | If they are not, then fix it because nothing below is going to work. You can also check the registration with: |
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| tkmedit bert orig.mgz -overlay f.nii.gz -overlay-reg register.dat | |
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| == Example 2 == Same as Example 1 but with a mask |
The register.dat will look something like this: |
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| mri_label2label --srclabel broca-fred.label --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod surface --hemi lh --srcmask fred-omnibus-sig 2 bfloat | bert |
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| This will load the bfloat data from fred-omnibus-sig and create a mask by thresholding the first frame absolute values at 2. To change it to only the positive values of the 3rd frame, add --srcmasksign pos --srcmaskframe 2 | 3.125 |
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| 5.000 | |
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| == Example 3 == You could also do the same mapping using talairach space as an intermediate: |
0.150000 |
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| mri_label2label --srclabel broca-fred.label --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod volume | 1.000000e+00 0.000000e+00 0.000000e+00 -2.252487e+00 |
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| Note that no hemisphere is specified with --regmethod volume. | 0.000000e+00 -8.902127e-01 4.555448e-01 2.342102e+00 |
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| == Example 4 == You have a label in the volume and you want to find the closest surface vertices: |
0.000000e+00 4.555449e-01 8.902128e-01 -2.159538e-01 |
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| mri_label2label --srclabel your.volume.label --s subject --trglabel lh.your.volume.on-pial.label --hemi lh --paint 30 pial --trgsurf pial | 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 |
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| This keeps the label on a single subject (but could also map to another subject). The label is mapped to vertices on the pial surface that are within 30mm of the label point. The xyz of the output label takes the coordinates of the pial surface (--trgsurf pial). | round * 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 * 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 * 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 * 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 |
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| When using volume registration method, you cannot specify the SUBJECTS_DIR on the command-line. | sinc interpolation is broken except for maybe COR to COR. |
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| [[label_area]], [[mri_mergelabels]] | [[mri_convert]] [[tkregister2]] |
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| BruceFischl |
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 |
--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
* 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
* 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
* 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
* 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
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>