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Hello Anderson,

I am trying to run MANOVA/MANCOVA (with contrasts of response variables). The following is the command that i am trying to execute.

palm -i all_FA_skeletonised_52pairs.nii -i all_MD_skeletonised_52pairs.nii -i all_MO_skeletonised_52pairs.nii -i all_MTR_skeletonised_52pairs.nii -m mean_FA_skeleton_mask.nii -d design.mat -con C.mset D.mset  -n 5000 -mv Wilks -o Wilks_TMV_myelin -save1-p -Tmv

The question that i am trying to answer is "is there a significant group difference with the combination where FA is high, MD is low, MTR is high"

My C.mset is (column 1= group1; column 2=group2; column3=nuisance_var1; column4=nuisance_var2)
======================
Matrix 2	4
-1	1	0	0
1	-1	0	0
======================
My D.mset is (column 1= modality1; column 2=modality2; column3=modality3; column4=modality4)
======================
Matrix 2	4
1	-1	0	1
1	-1	0	1
======================

i get the following error when i try the above (i do not get any error if i have only one row in my C.mset and D.mset files). How do i test for multiple contrasts ?
======================

Running PALM alpha53 using MATLAB with the following options:
-i all_FA_skeletonised_52pairs.nii
-i all_MD_skeletonised_52pairs.nii
-i all_MO_skeletonised_52pairs.nii
-i all_MTR_skeletonised_52pairs.nii
-m mean_FA_skeleton_mask.nii
-d design.mat
-con C.mset D.mset
-n 5000
-mv Wilks
-o Wilks_TMV_myelin
-save1-p
-Tmv
Reading input 1/4: all_FA_skeletonised_52pairs.nii
Reading input 2/4: all_MD_skeletonised_52pairs.nii
Reading input 3/4: all_MO_skeletonised_52pairs.nii
Reading input 4/4: all_MTR_skeletonised_52pairs.nii
Testing rank of the data for the MV tests. To skip, use -noranktest.
Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 50.1297 s
Number of possible permutations is 5.14951e+165.
Generating 5000 shufflings (permutations only).
Building null distribution.
0.005%	 [Design 1/1, Contrast 1/1, Shuffling 1/5000, Modality 1/4]
Warning: Rank deficient, rank = 4, tol =  5.992014e-13. 
> In palm_backend at 1259
  In palm at 80 
Warning: Matrix is singular to working precision. 
> In palm_backend>fastt at 2558
  In palm_backend>@(M,psi,res)fastt(M,psi,res,m,c,plm) at 929
  In palm_backend at 1293
  In palm at 80 
Error using  * 
Inner matrix dimensions must agree.

Error in palm_backend>fastt (line 2558)
den = sqrt(plm.eC{m}{c}'/(M'*M)*plm.eC{m}{c}*sum(res.^2)./df2);

Error in palm_backend>@(M,psi,res)fastt(M,psi,res,m,c,plm) (line 929)
                            fastpiv  {m}{c} = @(M,psi,res)fastt(M,psi,res,m,c,plm);

Error in palm_backend (line 1293)
                            [G{y}{m}{c},df2{y}{m}{c}] = fastpiv{m}{c}(M,psi,res);

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

Best
Jay