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## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting |
NAME bbregister |
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'''Index''' <<TableOfContents>> |
SYNOPSIS bbregister --s <subj> --mov <volid> --reg <regfile> \ --<contrast> |
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DESCRIPTION This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer. |
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= Name = command - 1/2 sentence summary |
POSITIONAL ARGUMENTS None |
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= Synopsis = command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4] |
REQUIRED FLAGGED ARGUMENTS --s subject FreeSurfer subject name as found in $SUBJECTS_DIR. |
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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) || |
--mov volid "Moveable" volume. This is the template for the cross-modal volume. Eg, for fMRI, it is the volume used for motion correction. |
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== Required Flagged Arguments == || --s subject || || FreeSurfer subject name || || --mov volid || || input/movable volume || || --reg register.dat || || output registration file || |
--reg register.{dat,lta} Output FreeSurfer registration file (tkregister-style or LTA format). |
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== Optional Flagged Arguments == || --nolog || no log file ||using this flag will not create a log file || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || = Outputs = || volume1 || description || || volume2 || description || |
--vsm VoxelShiftMap Include B0 distortion correction while performing registration. A voxel shift map can be created from a B0 map with the epidewarp.fsl script (in FreeSurfer) |
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= Description = type bbregister --help to get the full help on this. |
Initialization Arguments |
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= Examples = == Example 1 == |
--init-coreg (Default) Initialize the FreeSurfer mri_coreg program. |
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Intialize with FLIRT, view result with tkregister2: bbregister --s bert --mov func.nii --init-fsl --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf == Example 2 == Intialize with SPM, view result with tkregister2: bbregister --s bert --mov func.nii --init-spm --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf == Example 3 == Register a partial FoV using whole FoV as intermdediate: bbregister --s bert --mov partial.nii --init-fsl \ --int whole.nii --reg register.partial.dat tkregister2 --mov partial.nii --reg register.partial.dat --surf = Tips = When the registration fails, it could be because of a bad initialization. Check the first value in the mincost file. It will be at a value between 0 and 1.1, with 0 being perfect. Look at your good subjects to get an idea of what range to expect for your well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. = Bugs = None = See Also = [[othercommand1]], [[othercommand2]] = Links = FreeSurfer, FsFast = Methods Description = {{{ description description }}} = References = [[References/Lastname###]] = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> = Author/s = JaneSmith |
--no-coreg-ref-mask Do NOT use aparc+aseg.mgz as a reference mask. It will not attempt to use aparc+aseg if it is not there. |
NAME
- bbregister
SYNOPSIS
bbregister --s <subj> --mov <volid> --reg <regfile> \
--<contrast>
DESCRIPTION
- This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer.
POSITIONAL ARGUMENTS
- None
REQUIRED FLAGGED ARGUMENTS
- --s subject
FreeSurfer subject name as found in $SUBJECTS_DIR.
- "Moveable" volume. This is the template for the cross-modal volume. Eg, for fMRI, it is the volume used for motion correction.
Output FreeSurfer registration file (tkregister-style or LTA format).
--vsm VoxelShiftMap
- Include B0 distortion correction while performing registration. A voxel shift map can be created from a B0 map
with the epidewarp.fsl script (in FreeSurfer)
Initialize the FreeSurfer mri_coreg program.
- Do NOT use aparc+aseg.mgz as a reference mask. It will not attempt to use aparc+aseg if it is not there.