Dear Anderson Winkler,

I am trying to run a 2x2 mixed-effects ANOVA (group x time (40 subjects)) in PALM. Using the "design_ekaterina.ods" example I set up 2 corresponding design matrices (attached) with 2 t-contrast and 2 F-contrast files.

Design and contrast files can be found in this dropbox folder: https://www.dropbox.com/sh/te4humtaiklijq5/AABcg2Jj0gfDSablekV0h8baa?dl=0

I run PALM (a115) under Matlab2018b with FSL 6.0.1 by using the following command:

palm -i subjects_data.nii ...

         -m mask.nii ...

         -d design_temporal.mat ...

         -t design_temporal_tcon.con ...

         -f design_temporal.con ...

         -d design_group.mat ...

         -t design_group_tcon.con ...

         -f design_group.con ...

         -eb EB.grp ... 

         -n 10000 ...

         -T ...

         -whole ...

         -within ...

         -corrcon ...

         -logp ...

         -o palm_anova

The first warning I received immediately is: 

Warning: You chose to correct over contrasts, or run NPC

         between contrasts, but with the design(s) and,

         contrasts given it is not possible to run

         synchronised permutations without ignoring repeated

         elements in the design matrix (or matrices). To

         solve this, adding the option "-cmcx" automatically.

After running the first contrasts for the first design matrix I get the following errors:

0.00111% [Shuffling 1/10000, Design 1/2, Contrast 1/6, Modality 1/1]

Saving file:  palm_anova_vox_tstat_d1_c1

0.00222% [Shuffling 1/10000, Design 1/2, Contrast 2/6, Modality 1/1]

Saving file:  palm_anova_vox_tstat_d1_c2

0.00333% [Shuffling 1/10000, Design 1/2, Contrast 3/6, Modality 1/1]

Saving file:  palm_anova_vox_tstat_d1_c3

0.00444% [Shuffling 1/10000, Design 1/2, Contrast 4/6, Modality 1/1]

Saving file: palm_anova_vox_tstat_d1_c4

0.00556% [Shuffling 1/10000, Design 1/2, Contrast 5/6, Modality 1/1]

Warning: Rank deficient, rank = 42, tol =  1.962050e-13. 

> In palm_core (line 1417)

  In palm (line 81)

  In palm_run (line 9)

 

Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND =

1.945966e-18. 

> In palm_core>fastt (line 2749)

  In palm_core (line 1469)

  In palm (line 81)

  In palm_run (line 9)

 

Error using  * 

Incorrect dimensions for matrix multiplication. Check that the number of columns in the

first matrix matches the number of rows in the second matrix. To perform elementwise

multiplication, use '.*'.

Error in palm_core>fastt (line 2749)

den = sqrt(plm.mrdiv(plm.eC{y}{m}{c}{o}',(M'*M))*plm.eC{y}{m}{c}{o}*sum(res.^2)./df2);

Error in palm_core (line 1469)

                                [G{y}{m}{c},df2{y}{m}{c}] =

                                fastpiv{m}{c}(M,psi,res,y,m,c,1,plm);

Error in palm (line 81)

palm_core(varargin{:});

Error in palm_run (line 9)

palm -i

subjects_data.nii

...

It seems to me that I specified the F-contrasts incorrectly. But I don't know how else I would specify them? 

I would be very glad for any help on the correct setup of this analysis!

Cheers,

Paul