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command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4] | autoreg-sess -s [subjectname] -d [subjectdirectory] |
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|| argA || brief description || detailed description (eg, help file information) || || argB || brief description || detailed description (eg, help file information) || |
none |
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|| -flag1 arg1 || brief description || detailed description (eg, help file information) || || -flag2 arg2 || brief description || detailed description (eg, help file information) || |
|| -s sessid or -sf sessidfile || subject name or name of text file containing list of subjects || || -d srchdir or -df srchdirfile || name of subject directory || |
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|| -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || |
|| -fsd dir || functional subdirectory (bold)|| || -asd dir || anatomical subdirectory (3danat) || || -anatrun run || anatomical run to use for aligment (auto) || || -sessanat || register to same session anatomical || || -unmask mask || set unix file permission mask || || -version || print version and exit || |
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|| volume1 || description || || volume2 || description || |
|| register.dat || in each subject's bold directory || |
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command foo -i f -o out | autoreg-sess -s subject1 -d . (if in subject_dir) |
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["othercommand1"], ["othercommand2"] | ["tkregister-sess"], ["tkregister2"] |
Navigation(children) Index TableOfContents
Name
autoreg-sess
Synopsis
autoreg-sess -s [subjectname] -d [subjectdirectory]
Arguments
Positional Arguments
none
Required Flagged Arguments
-s sessid or -sf sessidfile |
subject name or name of text file containing list of subjects |
-d srchdir or -df srchdirfile |
name of subject directory |
Optional Flagged Arguments
-fsd dir |
functional subdirectory (bold) |
-asd dir |
anatomical subdirectory (3danat) |
-anatrun run |
anatomical run to use for aligment (auto) |
-sessanat |
register to same session anatomical |
-unmask mask |
set unix file permission mask |
-version |
print version and exit |
Outputs
register.dat |
in each subject's bold directory |
Description
autoreg-sess works in two stages. First, it aligns the same-session anatomical to the FreeSurfer anatomical. Next, it computes the registration from the functional to the same-session anatomical based only on the geometry of the acquisition. It then concatenates the two to give the registration from the functional to the FreeSurfer anatomical. Because the second func-anat reg is based only on header information, an movement between the functional and the same-session anatomical will not be compensated for.
Examples
Example 1
autoreg-sess -s subject1 -d . (if in subject_dir)
description
Example 2
command foo -i f -o out -f fvalue
description
Bugs
None
See Also
["tkregister-sess"], ["tkregister2"]
Links
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>