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| '''Index''' <<TableOfContents>> | |
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| '''Index''' <<TableOfContents>> |
= 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 == ||--mov 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. || ||--template 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. || |
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| = 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. |
== 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: $SUBJECTS_DIR/$subjid/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 (most up-to-date) help and exit || || |
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| = Synopsis = mri_cvs_register--mov arg1 --template arg2 |
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| = Arguments = == Positional Arguments == || argA || brief description || detailed description (eg, help file information) || || argB || brief description || detailed description (eg, help file information) || == Required Flagged Arguments == || -flag1 arg1 || brief description || detailed description (eg, help file information) || || -flag2 arg2 || brief description || detailed description (eg, help file information) || == Optional Flagged Arguments == || -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || |
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| || volume1 || description || || volume2 || description || |
See below. |
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| description | The CVS registration stream consists of 3 steps: (1) surface-based registration, (2) elastic registration and (3) volumetric registration. 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, but the (i) step could be eliminated if quicker execution time is required by using the "--noaseg" flag. |
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| = Examples = == Example 1 == command foo -i f -o out |
Relevant files that you should have in your directory (most recent on the top and the oldest in the bottom): |
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| description | (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) |
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| == Example 2 == command foo -i f -o out -f fvalue |
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 |
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| description | 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) and (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 ************ Note, the longest processing step in the CVS pipeline at the moment is the volumetric registration which might take about 15 hrs. The rest takes about 2 hours. ************ You will not be able to use fsaverage as a template as it does not have a corresponding surface and volumetric atlas. Instead, you can use one of the CVS atlases as a template (cvs or cvs_mni152). |
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| [[othercommand1]], [[othercommand2]] | [[mris_register]], [[mri_nl_align]], [[mris_resample]], [[mri_cvs_check]], [[mri_cvs_data_copy]] |
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| FreeSurfer, FsFast = Methods Description = {{{ description description }}} |
FreeSurfer |
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| [[References/Lastname###]] | 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 |
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| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | Report bugs to < analysis-bugs@nmr.mgh.harvard.edu > |
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| JaneSmith | LillaZollei |
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
--mov 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. |
--template 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: $SUBJECTS_DIR/$subjid/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 (most up-to-date) 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 registration. 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, but the (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) and (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
************
Note, the longest processing step in the CVS pipeline at the moment is the volumetric registration which might take about 15 hrs. The rest takes about 2 hours.
************
You will not be able to use fsaverage as a template as it does not have a corresponding surface and volumetric atlas. Instead, you can use one of the CVS atlases as a template (cvs or cvs_mni152).
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 >