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| ##||Up to FreeviewGuide ||Back to [[FreeviewGuide/FreeviewWorkingWithData/PointSet|PointSet]] ||Continue to [[FreeviewGuide/FreeviewTools|FreeviewTools]] || |
||Up to FreeviewGuide ||Back to [[FreeviewGuide/FreeviewWorkingWithData/PointSet|PointSet]] ||Continue to [[FreeviewGuide/FreeviewTools|FreeviewTools]] || '''Index''' <<TableOfContents>> = Name = == fvcompare == Freeview Compare is a script that can assist in the visualization of two subjects. These can be two time points of the same subject or the same subject analyzed in two different ways (eg. using Freeview dev version vs Freeview stable). The script will simultaneously load the volumes, segmentations and surface data from two subjects in freeview, and can name them with different prefixes for easier visualization. The two subjects can be in the same, or different SUBJECTS_DIRs. '''Note:''' No registration is applied. = Command = fvcompare --s1 <subject1> --s2 <subject2> [options] = Optional Flags = || --s || coming soon || || --sd1, --sd2 || location of subjects_dir for subject 1 or subject 2) || || --n1 || the prefix for subject1 files (default is s1) || || --n2 || the prefix for subject2 files (default is s2) || || --vol || volname (as found in subject/mri; default is orig.mgz, can have multiple) || || --seg || segname (as found in subject/mri; default is arapc+aseg.mgz can have multiple) || || --no-seg || do not display segmentations || || --lh, --rh || display only left or right hemi || || --no-surf || do not display surfaces || || --gray min max || set gray scale levels (default is 0 255) || |
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##== Freeview Compare == ##Freeview Compare is a script that can assist in the visualization of two subjects. These can be two time points of the same subject, or the same subject analyzed in two different ways (eg using Freeview dev version vs Freeview stable). The script ##will simultaneously load the volume, segmentation and surface data from two subjects in freeview. The two subjects can be in the same, or different SUBJECTS_DIRs. No registration is applied. |
= Examples = |
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##== Synopsis == ##fvcompare |
'''If the two subjects are in the same SUBJECTS_DIR''' {{{ fvcompare --s1 subject1 --s2 subject2 --n1 tp1 --n2 tp2 }}} Where subject1 will have files prefixed with "tp1" in freeview and subject2 will have files prefixed with "tp2." |
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'''If the two subjects are in different SUBJECTS_DIR''' {{{ fvcompare --s1 subject1 --sd1 DEV_SUBJECTS_DIR --s2 subject2 --sd2 STD_SUBJECTS_DIR --n1 dev --n2 stable }}} "--sd1" defines the SUBJECTS_DIR for subject1, and "--sd2" defines the SUBJECTS_DIR for subject2. Subject1 files will have the prefix "dev" and subject2 files will have the prefix "stable." '''If the subjects have the same name but in different SUBJECTS_DIR''' {{{ fvcompare --s subject --sd1 SUBJECTS_DIR1 --sd2 SUBJECTS_DIR2 }}} <explanation coming soon> |
Up to FreeviewGuide |
Back to PointSet |
Continue to FreeviewTools |
Index
Contents
Name
fvcompare
Freeview Compare is a script that can assist in the visualization of two subjects. These can be two time points of the same subject or the same subject analyzed in two different ways (eg. using Freeview dev version vs Freeview stable). The script will simultaneously load the volumes, segmentations and surface data from two subjects in freeview, and can name them with different prefixes for easier visualization. The two subjects can be in the same, or different SUBJECTS_DIRs.
Note: No registration is applied.
Command
fvcompare --s1 <subject1> --s2 <subject2> [options]
Optional Flags
--s |
coming soon |
--sd1, --sd2 |
location of subjects_dir for subject 1 or subject 2) |
--n1 |
the prefix for subject1 files (default is s1) |
--n2 |
the prefix for subject2 files (default is s2) |
--vol |
volname (as found in subject/mri; default is orig.mgz, can have multiple) |
--seg |
segname (as found in subject/mri; default is arapc+aseg.mgz can have multiple) |
--no-seg |
do not display segmentations |
--lh, --rh |
display only left or right hemi |
--no-surf |
do not display surfaces |
|| --gray min max || set gray scale levels (default is 0 255) ||
Examples
If the two subjects are in the same SUBJECTS_DIR
fvcompare --s1 subject1 --s2 subject2 --n1 tp1 --n2 tp2
Where subject1 will have files prefixed with "tp1" in freeview and subject2 will have files prefixed with "tp2."
If the two subjects are in different SUBJECTS_DIR
fvcompare --s1 subject1 --sd1 DEV_SUBJECTS_DIR --s2 subject2 --sd2 STD_SUBJECTS_DIR --n1 dev --n2 stable
"--sd1" defines the SUBJECTS_DIR for subject1, and "--sd2" defines the SUBJECTS_DIR for subject2. Subject1 files will have the prefix "dev" and subject2 files will have the prefix "stable."
If the subjects have the same name but in different SUBJECTS_DIR
fvcompare --s subject --sd1 SUBJECTS_DIR1 --sd2 SUBJECTS_DIR2
<explanation coming soon>