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

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

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

DougGreve

-Deletions are marked like this.
+Additions are marked like this.
 Line 18:
-command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]
+autoreg-sess -s [subjectname] -d  [subjectdirectory]
 Line 22:
-|| argA || brief description || detailed description (eg, help file information)  ||

|| argB || brief description || detailed description (eg, help file information)  ||
+none
-Line 26:
+Line 25:
-|| -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 ||
 Line 30:
-|| -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 ||
-Line 34:
+Line 38:
-|| volume1 || description ||

|| volume2 || description ||
+|| register.dat || in each subject's bold directory ||
-Line 49:
+Line 52:
-command foo -i f -o out
+autoreg-sess -s subject1 -d . (if in subject_dir)
-Line 62:
+Line 65:
-["othercommand1"], ["othercommand2"]
+["tkregister-sess"], ["tkregister2"]