On 6/19/14 3:57 PM,
DeCross, Stephanie N. wrote:
Hi,
I’m having trouble figuring out the correct way
to weight my conditions with mkcontrast for a couple
of complicated contrasts I’m making.
I have six conditions:
#1 female face approach
#2 male face approach
#3 female face withdraw
#4 male face withdraw
#5 car approach
#6 car withdraw
For a couple of contrasts, I had to manually
weight with -wcond. For this first one, everything
worked. First I made an all faces (male and female,
approaching or withdrawing) v. fixation (face_v_fix)
contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made
an all cars (approaching or withdrawing) v. fixation
(car_v_fix) contrast, weighted -a 5 -a 6. To make my
contrast face_v_car, which is a subtraction of the
above two contrasts, I used the command:
mkcontrast-sess -contrast face_v_car -analysis
5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25
0.25 -0.5 -0.5. When I extracted the data in an ROI
analysis for these three contrasts and a bunch
others, I manually checked all ROI values for a
given subject. The values for my face_v_fix and
car_v_fix are correct, and when I manually subtract
those two values, it gives me a value identical to
the value that derives from the contrast itself.
This is as it should be, as they’re two methods of
computing the same thing.
My problem is with a similar trio of contrasts.
My contrast for all faces (both male and female)
approaching minus all faces (male and female)
withdrawing (aka face-aw), which is weighted -a 1 -a
2 -c 3 -c 4 in the mkcontrast command, and my car
approaching minus car withdrawing contrast (aka
car-aw), which is weighted -a 5 -a 6, are both fine.
I’m trying to make a contrast face-aw minus car-aw
(aka face-aw_v_car-aw), which essentially involves a
double subtraction (faces approaching minus faces
withdrawing, MINUS cars approaching vs. cars
withdrawing) in which the face-aw part involves 4
conditions because of the two genders of faces but
the car-aw part involves only 2. The command I used
was: mkcontrast-sess -contrast face-aw_v_car-aw
-analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond
0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the
ROI data, the values for my face-aw and car-aw
contrasts were correct, but when I manually subtract
them the value is different from the value that
derives from the face-aw_v_car-aw contrast itself,
when it should be equivalent. I have no idea why
it’s not working.
The only thing I can think that would affect this
and mess it up is my weighting in the mkcontrast
command. Do you know if I’m using the wrong
weighting numbers or missing a flag I need or if
there's some way to configure the contrast
differently I should be doing? I’m sorry if I
provided way more information than I needed to or
not nearly enough; I’m very new at all things
FreeSurfer and finding that the learning curve can
be challenging.
Thanks so much,
Stephanie
Stephanie N. DeCross
Clinical Research Coordinator
Psychiatric Neuroimaging Research Program
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA 02129
Phone: 617-724-3283
Fax: 617-726-4078