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 the
.mgz file you'd like to see. After loading there will be a button
"Configure overlay" that opens a window where the colourbar can be set,
etc. For 0.05 the threshold would be -log10(0.05) = 1.301.
Hope this helps.
All the best,
On 15 September 2016 at 19:46, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote:
> 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 is similar to qdec
> I believe), however I have not been able to load the stats files
> correctly. The output of palm is lh.thickness_tfce.mgz for my various
> 1) Is .mgz the proper format for the stats files or do I need to convert
> this to another type like .mgh etc?
> 2) Can I display this in freeview or is another program needed? I also
> tried tksurfer but when I loaded the stats file as an overlay nothing
> displayed. I want to make sure that the stats is loaded as an overlay in
> freeview/tksurfer and if so, do I need to select anything special so that
> it scales the logp values correctly?
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