I've just replied to this in the HCP list (and will update here too when the documentation is ready).

On 14 September 2016 at 18:28, Michael F.W. Dreyfuss <[log in to unmask]> wrote:

Hello, I am trying to run palm on cifti data with TFCE to find mean activation across a group. When I use the -T flag, the program crashed with the error:

Command:
palm -i ${ContrastName}.dtseries.nii  -transposedata  -d $LevelThreeFEATDir/design.mat  -o $ContrastName -t /tmp/CtxFGNG/CtxFGNG_Level3_Analysis/desion -T -ise

Error:
0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1]
Saving file: FoodNogo_dat_tstat
Index exceeds matrix dimensions.

Error in palm_tfce (line 77)
    elseif plm.Yisvtx(y) || plm.Yisfac(y),

Error in palm_core (line 1680)
                                Gtfce{y}{m}{c} = tfcefunc(G{y}{m}{c},y,opts,plm);

Error in palm (line 81)
palm_core(varargin{:});


Alternatively, if I use the same command, but replace -T with -fdr, the program runs smoothly, so I do not think the problem is with my design files or data unless they need to be generated in a special way for TFCE using palm. Are there any recommendation or previous examples of how I can use TFCE on cifti data using palm?

Any help on this is very appreciated.

Thank you,
Michael