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
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#F-Tests_.28Inter-Group_differences.2C_no_repeated_measures.29>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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