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Hello all,
Never mind, I just figured it out.
However, I have another question regarding using PALM for FreeSurfer. If I am not mistaken, CFT < 0.05 is OK to report if I use permutation method (PALM). Please correct me if CFT < 0.05 is not acceptable here. I was wondering if there is any difference in following two commands (A and B): As Z-score corresponding to p = 0.05 is 1.64 i.e., qnorm(1-10^-1.3)=1.64 for one-tailed and Z-score corresponding to p = 0.05 is 1.95 i.e., qnorm(1-10^-1.3/2)=1.95 for two--tailed)
(A). palm -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT *-C 1.64* -twotail -n 5000 -nouncorrected and (B). palm -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT *-C 1.95* -onetail -n 5000 -nouncorrected
In other words, I was wondering if these two options: (A). I use -C as 1.64 in addition to the flag twotail and (B). I use -C as 1.95 in addition to the flag onetail are identical? i.e., isn't that true that if I use -C 1.95 in addition to the flag twotail - this will apply two-tailed twice?
Also, I was wondering how can I apply Bonf. Corr. for two hemispheres in the above command, or by-default this is already applied?
Thanks.
On Tue, Jan 7, 2020 at 12:30 PM Martin Juneja mj70481@gmail.com wrote:
Hi,
I am trying to run PALM in MATLAB. After I run the following command, I get following error: palm -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT -C 1 -twotail -n 1000 -nouncorrected
Running PALM alpha116 using MATLAB 9.6.0.1072779 (R2019a) with the following options: -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT -C 1 -twotail -n 1000 -nouncorrected -noniiclass Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh Reading input 1/1: SPSX/lh.SPS_vol.10.mgh Dot indexing is not supported for variables of this type.
Error in palm_takeargs (line 1679) if any(size(plm.srf{s}.data.vtx,1) == ...
Error in palm_core (line 33) [opts,plm] = palm_takeargs(varargin{:});
Error in palm (line 81) palm_core(varargin{:});
Any help in resolving this issue would be really appreciated.
Thanks.