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

--srcsubject srcsubject

source subject

Optional Flagged Arguments

--hemi hemisphere

(lh or rh)

required with --regmethod surface

Outputs

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>

-Deletions are marked like this.
+Additions are marked like this.
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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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-|| --srclabel srclabelfile || input label file ||

|| --trgsubject trgsubject || target subject ||

|| --trglabel trglabel     || output label file] ||

|| --regmethod registrationmethod ||  Legal values: surface, volume ||
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-|| --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 ||
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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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-. 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 



 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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-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