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Freeview Compare

Freeview Compare is a script that can assist in the visualization of up to four 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.


fvcompare --s1 <subject1> --s2 <subject2> [options]

Optional Flags

--sd1, --sd2, --sd3, --sd4

location of subjects_dir for subject 1 or subject 2)


sets both subject1 and subject2 to "subject"

--n1, --n2, --n3, --n4

the prefix for each subject's files in freeview (default is s1, s2, s3, and s4)


volname (as found in subject/mri; default is orig.mgz, can have multiple)


segname (as found in subject/mri; default is arapc+aseg.mgz can have multiple)

|| --c1, --c2, --c3, --c4 || specifies the color of each subject's surfaces ||


do not display segmentations

--lh, --rh

display only left or right hemi


do not display surfaces

--gray min max

set gray scale levels (default is 0 255)


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

The "--s" flag sets both subject1 and subject2 to "subject." This would be ideal in a situation where there are two SUBJECT_DIRs with the same subjectid in each. For example, if you had the same subject analyzed with two versions of FreeSurfer, and you saved your results from each version in a different location.