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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 four time points of the same subject or the same subject analyzed in multiple ways (such as Freeview dev version vs Freeview stable etc.). The script will simultaneously load the volumes, segmentations and surface data from four subjects in freeview, and can name them with different prefixes for easier visualization. The subjects can be in the same, or different SUBJECTS_DIRs.

Note: No registration is applied.


fvcompare --s1 <subject1> --s2 <subject2> --s3 <subject3> --s4 <subject4> [options]

Optional Flags

--n1 <name1>, --n2 <name2> ...

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


location of SUBJECTS_DIR for each subject


sets the same name for all subjects (ex. if you have the same subjid but different SUBJECTS_DIRs

--vol <volname>

volume to load (as found in subject/mri; default is brainmask.mgz, can have multiple)

--seg <segname>

segmentation to load (as found in subject/mri; default is arapc+aseg.mgz, can have multiple)

--c1 <whitecolor1> <pialcolor1> --c2 <whitecolor2> <pialcolor2> ...

specifies the color of each subject's surfaces (if this flag is not used, colors are set for you)


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 --c1 green red --s2 subject2 --c2 blue yellow --n1 tp1 --n2 tp2 

Subject1 will have files prefixed with "tp1" in freeview and subject2 will have files prefixed with "tp2." The white surfaces for Subject1 will be colored green, and the pial surfaces will be colored red. The white surfaces for Subject2 will be blue and the pial surfaces will be yellow.

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 the name, "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.