Dear FSL experts, I would like to have your advice about a problem I am encountering using PALM. I am not very familiar with Palm thus I apologize in advance for a potential naive question. I am would like to investigate how 2 or 3 imaging metrics covariate across the whole brain (voxel-wise). In the FSL archive I found a previous conversation that provide a skeleton of what I could do: " If we want to estimate the interaction between modalities, should we transfer to joint inference (NPC or MANOVA/MANCOVA)? Just like FSLNets, explore the correlation between 2 RSN, using PALM to search the correlation between 2 modalities, for example, change of modality A causing positive/negative alteration of modality B? Yes, this is possible through the use of voxelwise EVs. This example, on whether modality A is associated/correlated with modality B, can be done using A as input (dependent variable, -i), and B as a voxelwise EV in the design (or vice-versa). It can be done in either PALM or randomise. And estimating the contribution of modality A and modality C to the alteration of modality B? Yes, also possible. For this, use B as input, and prepare two designs, one having A as voxelwise EV, another with C as voxelwise EV, then run these two designs in PALM with -corrcon, and at the end, use fslmaths to find the largest corrected p-value across both, which will indicate a conjunction(IUT in the paper ). Alternatively, for a joint test (UIT), use -npccon, that will do NPC over the contrasts for these two designs." Unfortunately I have some problem in implementing it. 1. I designed the .mat and .con file using the GLM GUI but my impression is that it allows to introduce voxelwise EVs only on top of a main EV. Is that correct? 2. I created the .mat and the .con file introducing Age as a main EV (I am in the context of an aging study) + the voxelwise EV matrix file: /NumWaves 2 /NumPoints 54 /PPheights 3.270000e+01 2.795043e-02 /Matrix -1.720000e+01 2.755630e-02 1.350000e+01 2.463088e-02 8.600000e+00 2.455896e-02 contrasts file: /ContrastName1 age /ContrastName2 fa /NumWaves 2 /NumContrasts 2 /PPheights 3.270265e+01 2.766217e-02 /RequiredEffect 2.066 0.607 /Matrix 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 After that, I run PALM with the following spec. # Configuration file for PALM. # Version alpha105, running in MATLAB 7.14.0.739 (R2012a). # 04-Apr-2017 14:05:50 -i all_brain_wqsm25.nii -evperdat all_FA.nii 2 1 -m c2_maxprob.nii -d Age_qsmFa.mat -t Age_qsmFa.con -T -demean -n 5000 -o qsmFa1 PALM routine starts: Reading input 1/1: all_brain_wqsm25.nii Reading EV per datum 1/1: all_FA.nii Reading design matrix and contrasts. Elapsed time parsing inputs: ~ 11.8342 seconds. Doing maths for -evperdat before model fitting: [Design 1/1, Contrast 1/2] (may take several minutes) Doing maths for -evperdat before model fitting: [Design 1/1, Contrast 2/2] (may take several minutes) Generating 5000 shufflings (permutations only). Building null distribution. 0.01% [Design 1/1, Contrast 1/2, Shuffling 1/5000, Modality 1/1] But then I got the following warning several times: Warning: Rank deficient, rank = 1, tol = 1.046556e-13. > In palm_core at 1406 In palm at 81 Until the routine stopped after several iteration of the following warning: Warning: Matrix is singular to working precision. > In palm_core>fastt3d at 2749 In palm_core at 1462 In palm at 81 Saving file: qsmFa1_vox_tstat_c1 Error using betainc X must be in the interval [0,1]. Error in palm_gcdf (line 63) gcdf(ig) = betainc(1./(1+G(ig).^2./df2(ig)),df2(ig)/2,.5)/2; Error in palm_gtoz (line 80) Z(~idx) = -erfcinv(2*palm_gcdf( G(~idx),1,df2(~idx)))*sqrt(2); Error in palm_core (line 1592) G{y}{m}{c} = palm_gtoz(G{y}{m}{c},plm.rC0{m}(c),df2{y}{m}{c}); Error in palm (line 81) palm_core(varargin{:}); Any suggestions? As a note: when I tried the “equivalent” analysis with randomise_parallel (employing the same matrix and contrasts files) the routine run without producing warnings/errors. I would also very much appreciate any comments about what would be the best way to investigate how/where different MRI metrics (all registered to the same space) covariate. Thank you in advance for your help, Nicola