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If you want to reconstruct the resulting warp (as it was deleted to save space after the processing) and apply it to a new volume, you would need to call two functions. If the warp combined*tm3d does not exist run both (1) an d(2) , if it already exists, just run (2). (1) createMorph --out fullCVSmorph.tm3d --template template.mgz \ --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d (2) applyMorph --template template.mgz --transform fullCVSmorph.tm3d \ vol movingvol.mgz outputvol.mgz linear |
Index
Contents
Name
mri_cvs_register - registers MRI scans of two subjects (or a subject and the CVS atlas) using the combined volume and surface-based registration method, CVS. Make sure that SUBJECTS_DIR is properly set before calling this script!
Synopsis
mri_cvs_register--mov arg1 --template arg2
Arguments
Required Flagged Arguments
--template subjid |
subjid for subject to be moved / registered |
Subject id of the subject (as found in SUBJECTS_DIR) whose scan is to be moved in registration with that of the template. |
--mov subjid |
subjid for subject to be kept fixed (template) |
Subject id of the subject (as found in SUBJECTS_DIR) whose scan is to be used and the template / target for the registration. |
Optional Flagged Arguments
--outdir directory |
output directory where all the results are written |
Output directory where the resulting morphs should be written. NOTE, the morphs require quite a lot of space so make sure that there is enough disk space available before your analysis. The default location for the output is: SUBJECTS_DIR/mov/cvs |
--noaseg |
do not use aseg volumes in the registration pipeline (default is 0) |
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--nocleanup |
do not delete temporary files (default is 0) |
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--nolog |
do not produce a log file (default is 0) |
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--step1 |
only do step 1 (spherical registration) |
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--step2 |
only do step 2 (elastic registration) |
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--step3 |
only do step 3 (volumetric registration) |
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--version |
print version and exit |
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--help |
print help and exit |
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Outputs
See below.
Description
The CVS registration stream consists of 3 steps: (1) surface-based registration, (2) elastic registration and (3) volumetric regsitration. By default, in the current implementation of the script, step (3) consists of two steps: (i) registration using aseg volumes and (ii) registration using intensity volumes. This combination of the non-linear volumetric registrations proved to be very robust and accurate, butthe (i) step could be eliminated if quicker execution time is required by using the "--noaseg" flag.
Relevant files that you should have in your directory (most recent on the top and the oldest in the bottom):
(a) Full CVS (with both (i) and (ii)) nlalign-afteraseg-norm.m3z : the morph resulting from (ii) of step (3) (intensity-based non-linear registration); it is NOT combined with the elastic registration morph nlalign-afteraseg-norm.mgz : the morphed norm.mgz file; it is the final result of CVS and contains contributions from ALL registration steps (combination of the elatic morph and the two m3z files)
nlalign-aseg.m3z : the morph resulting from (i) of step (3) (aseg-based non-linear registration); it is NOT combined with the elastic registration morph nlalign-aseg.mgz : the morphed aseg.mgz file; it is the result of CVS up to (i) of step (3) and contains contributions from registration steps of the elatic morph and the above m3z file
el_reg_toTEMPLATE_aseg.mgz : the elastic morph applied to aseg.mgz el_reg_toTEMPLATE.tm3d : the elastic morph that combines correspondences recovered in steps (1) and (2) el_reg_toTEMPLATE.mgz : the elastic morph applied to norm.mgz
(b) shorter version of CVS (using only (ii) in step (3) of the algorithm):
nlalign-norm.m3z : the morph resulting from step(3) (intensity-based non-linear registration); it is NOT combined with the elastic registration morph nlalign-norm.mgz : the morphed norm.mgz file; it is the final result of CVS and contains contributions from ALL registration steps (combination of the elatic morph and the above m3z file)
el_reg_toTEMPLATE.tm3d : the elastic morph that combines correspondences recovered in steps (1) and (2) el_reg_toTEMPLATE.mgz : the elastic morph applied to norm.mgz
If you ran the mri_cvs_registration script with the "--nocleanup" option then you will see two more files called combined*tm3d. These files take up a lot of memory so by default are deleted. They can be recreated in case the cvs morph needs to be applied to another volume at a later time. The morphs left behind when using the "--nocleanup" option are:
(a) el_reg_toTEMPLATE.tm3d : the elastic morph that combines correspondences recovered in steps (1) and (2) combined_elreg_aseg.tm3d : the morph that combines correspondences recovered in steps (1), (2) and (3) (i) combined_elreg_afteraseg-norm.tm3d : the morph that combines correspondences recovered in steps (1), (2), (3) (i) and (3) (ii) (b) el_reg_toTEMPLATE.tm3d : the elastic morph that combines correspondences recovered in steps (1) and (2) combined_elreg_norm.tm3d : the morph that combines correspondences recovered in steps (1), (2) and (3) (ii)
If you want to reconstruct the resulting warp (as it was deleted to save space after the processing) and apply it to a new volume, you would need to call two functions. If the warp combined*tm3d does not exist run both (1) an d(2) , if it already exists, just run (2).
(1) createMorph --out fullCVSmorph.tm3d --template template.mgz \
- --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d
(2) applyMorph --template template.mgz --transform fullCVSmorph.tm3d \ vol movingvol.mgz outputvol.mgz linear
Bugs
None
See Also
mris_register, mri_nl_align, mris_resample, mri_cvs_check, mri_cvs_data_copy
Links
References
G.M. Postelnicu*, L. Zöllei*, B. Fischl: "Combined Volumetric and Surface Registration", IEEE Transactions on Medical Imaging (TMI), Vol 28 (4), April 2009, p. 508-522
L. Zöllei, A. Stevens, K. Huber, S. Kakunoori, B. Fischl: "Improved Tractography Alignment Using Combined Volumetric and Surface Registration", NeuroImage 51 (2010), 206-213
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>