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 /ContrastName10 HC/Grp2 M/F Interaction /ContrastName11 Grp1/Grp2 M/F Interaction /NumWaves 9 /NumPoints 11 /Matrix 1 1 -1 -1 0 0 0 0 0 -1 -1 1 1 0 0 0 0 0 1 1 0 0 -1 -1 0 0 0 -1 -1 0 0 1 1 0 0 0 0 0 1 1 -1 -1 0 0 0 0 0 -1 -1 1 1 0 0 0 1 -1 1 -1 1 -1 0 0 0 -1 1 -1 1 -1 1 0 0 0 1 -1 -1 1 0 0 0 0 0 1 -1 0 0 -1 1 0 0 0 0 0 1 -1 -1 1 0 0 0
My colums correspond to the following: EV1:HC-M EV2:HC-F EV3:Grp1-M EV4:Grp1-F EV5:Grp2-M EV6:Grp2-F EV7:Age EV8:Education EV9:Disease Severity In the folder I was running the analysis I put the lh.thickness.10mm.mgz, rh.thickness.10mm.mgz, lh.white (fsaverage), rh.white (fsaverage), lh.mask.mgh (taken from running qdec initially), rh.mask.mgh (taken from running qdec initially). I initially ran palm_hemimerge lh* within matlab Then from a terminal I ran the following command: palm -i bh.thickness.10mm.mgz -d design.mat -t design.con -o bh.thickness -n 500 -approx tail -corrcon -s bh.white -T -tfce2D -logp -m bh.mask.mgz -nouncorrected The command ran fully. When I loaded contrast 6 I found no results on the pial surface, however the white matter surface (where the mask was) was speckled all over with no cluster. If there is a location,I can upload the stats file if that is easier. Thanks, Ajay On Sat, Sep 17, 2016 at 10:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > 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 > was wrong. Therefore it seems to only run permutation testing on the > surface of the white matter. Due to the fact that it is unsmoothed white > matter, I think this is why we see some speckling bleeding through near the > boundaries > > In order to do permutation testing accurately for surface based cortical > thickness, would the mask need to be a volume file which is between the > pial and white matter surfaces or would it just need to be the pial surface > (lh.pial / rh.pial), or something else? Any suggestions on the best way to > create this? > > Thanks, > Ajay > > On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> 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 >> was wrong. Therefore it seems to only run permutation testing on the >> surface of the white matter as seen in the attached photo. Due to the fact >> that it is unsmoothed white matter, I think this is why we see some >> speckling bleeding through near the boundaries >> >> In order to do permutation testing accurately for surface based cortical >> thickness, would the mask need to be a volume file which is between the >> pial and white matter surfaces or would it just need to be the pial surface >> (lh.pial / rh.pial), or something else? Any suggestions on the best way to >> create this? >> >> Thanks, >> Ajay >> >> >> >> >> On Thu, Sep 15, 2016 at 1:46 PM, 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 >>> contrasts. >>> >>> 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? >>> >>> Thanks, >>> Ajay >>> >> >> >
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