Hi Ajay,
Make sure you have to run palm_hemisplit on the outputs first, i.e.:
palm_hemisplit bh.thickness_*
Note that the "-o bh.thickness" was a somewhat poor choice of outputs as
now it's necessary to use the underscore ("_") to avoid overwriting
original inputs; for future runs, consider some
Hi Anderson,
My full design contrasts are below:
/ContrastName1 HC > Grp1
/ContrastName2 HC < Grp1
/ContrastName3 HC > Grp2
/ContrastName4 HC < Grp2
/ContrastName5 Grp1 > Grp2
/ContrastName6 Grp1 < Grp2
/ContrastName7 M > F
/ContrastName8 M < F
/ContrastName9 HC/Grp1 M/F Interaction
/ContrastNa
Hi Ajay,
The mask is a file of the "curvature" type, that is, it contains vertexwise
data, and should mask out the "unknown" region (that region in the medial
aspect that is not cortex and is there to ensure the topology is the same
as that of a sphere). The mask can alternatively be a .mgz file a
Hi Anderson,
Thanks for the help. When viewing my results they looked very strange.
Upon further investigation it looks as though the mask I supplied to PALM
was a white matter mask (mask.mgh from running qdec initially) created when
I ran qdec. I assumed this would be the whole cortex but I w
Hi Ajay,
To open the .mgz files produced by PALM you would first load the surface in
FreeView (at the top of the left panel, click on "Surface" then on the
button with a "+" sign), then after the surface has been loaded, in the
menu "Overlay" in the left panel, select "Load generic..." and load th
Hello Freesurfer Experts,
I was running permutation simulations on cortical thickness data and I
had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I
then tried FSL's PALM which is an extension of randomize to calculate
threshold free stats. I saved the output as logp(which
