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.

Links

FreeSurfer, FsFast

Methods Description

References

Reporting Bugs

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

-  ⇤ ← Revision 1 as of 2017-10-03 16:13:24 → 
  Size: 6014
  Editor: MorganFogarty
  Comment:
+   ← Revision 3 as of 2017-10-03 16:43:57 → ⇥
  Size: 3470
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 14:
-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).
 Line 17:
-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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+Line 21:
-|| --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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+Line 25:
-|| --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||
||
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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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+Line 63:
-. 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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+Line 67:
-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 

 mri_label2label --srclabel broca-fred.label  --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod surface --hemi lh

This will map from fred to sally using sphere.reg. The registration surface can be changed with --surfreg.


== Example 2 ==
Same as Example 1 but with a mask

 mri_label2label --srclabel broca-fred.label  --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod surface --hemi lh --srcmask  fred-omnibus-sig 2 bfloat 

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   


== Example 3 ==
You could also do the same mapping using talairach space as an intermediate:

    mri_label2label --srclabel broca-fred.label  --srcsubject fred --trglabel broca-sally.label --trgsubject sally --regmethod volume

Note that no hemisphere is specified with --regmethod volume.

== Example 4 ==
You have a label in the volume and you want to find the closest surface vertices:

   mri_label2label --srclabel your.volume.label --s subject --trglabel lh.your.volume.on-pial.label --hemi lh --paint 30 pial --trgsurf pial

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).
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+Line 69:
-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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+Line 72:
-[[label_area]],  [[mri_mergelabels]]
+[[mri_convert]] [[tkregister2]]
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+Line 86:
-BruceFischl