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.