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Dear Anderson, 

Thank you so much for your swift and helpful response!

As you suggested, I tried to run palm using both model 2 and 3. However, MATLAB seems to be unable to adequately read the design matrix, giving me the error as displayed below. Randomise does successfully run on exactly the same .mat and .con files (also attached) and the wiki says that palm should also run on these (fsl vest) files. 

Do you have an idea why this error comes up?

Thanks again!

Marsh Königs


While trying to figure out what I am doing wrong, I simplified the palm command to test only 1 model until palm works correctly:

/usr/local/fsl/palm-alpha57/palm -i all_FA_skeletonised.nii.gz -m mean_FA_mask.nii.gz -d palm6.mat -t palm6.con -T -corrcon -o palm -noniiclass 
Running PALM alpha57 using MATLAB with the following options:
-i all_FA_skeletonised.nii.gz
-m mean_FA_mask.nii.gz
-d palm6.mat
-t palm6.con
-T
-corrcon
-o palm
-noniiclass
Found FSL in /usr/local/fsl
Reading input 1/1: all_FA_skeletonised.nii.gz
Reading design matrix and contrasts.
Error using reshape
To RESHAPE the number of elements must not change.

Error in palm_vestread (line 55)
M = reshape(M,[nW,nP])';

Error in palm_miscread (line 79)
        [X.data,X.extra.PPH] = palm_vestread(X.filename);

Error in palm_takeargs (line 1980)
        Mtmp = palm_miscread(opts.d{m});

Error in palm_backend (line 32)
[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 80)
palm_backend(varargin{:});