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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

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)

--nocleanup

do not delete temporary files (default is 0)

--nolog

do not produce a log file (default is 0)

--step1

only do step 1 (spherical registration)

--step2

only do step 2 (elastic registration)

--step3

only do step 3 (volumetric registration)

--version

print version and exit

--help

print help and exit

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

FreeSurfer

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>

Author/s

LillaZollei

mri_cvs_register (last edited 2018-02-05 12:34:44 by MorganFogarty)