Hi Gabriela,

PALM is expecting files with the following dimensions:

input => nS x nV

design => nS x nR

contrast => nC x nR

where

nS = number of subjects

nV = number of image points

nR = number of regressors in the design matrix

So, if you transpose your design matrix and contrast matrix, it should work. About the ftests.csv, it is also a contrast matrix, thus it has also to be a nR x nC matrix.

If you're following the GLM example in the FSl webpage, you can use the matrix

1 0 0 0 0 0 0 0

0 1 0 0 0 0 0 0

0 0 1 0 0 0 0 0

If you're testing for differences between groups This older thread might help you setup your F-tests: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;3846fd1a.1910

All the best,

Bianca

Em qua, 30 de out de 2019 às 09:51, Gabriela Dzięgiel <[log in to unmask]> escreveu:

Hello!

Unfortunately, I am not an FSL user and so despite reading through PALM and FSL GLM Guide I don't know where I am going wrong. I want to condunct PALM analysis, correcting for multiple contrasts (the aim is also to control for several modalities but for now I'm just trying to make the toolbox work). I use the following command:

palm -i input.csv -d design.csv -t contrasts.csv -f ftests.csv -fonly -corrcon -n 100

and I get the following error message:

Reading input 1/1: input.csv
Reading design matrix and contrasts.
Index exceeds matrix dimensions.

Error in palm_takeargs (line 2308)
rC1 = plm.rC{1}(1);

Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});

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

I am really confused because my csv files seem to have the right dimensions (input: 120x163842; design: 120x8; contrasts: 3x8; ftests: 3x3). They are csv files separated with spaces.

Can anybody give me any clue on what is wrong with my command or with design, contrasts, etc. files? I would be very grateful!

Best regards,
Gabriela Dzięgiel-Fivet

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