Hi David,

You'd break in a per-space basis, i.e.:

palm('-i','data/4D_1.nii','-m','data/mask_1.nii','-d','data/designmatrix_1.csv','-data/contrasts_1.csv','-n',10000,'-T','-corrcon','-o','data');

Another possibility that is useful when just a few options change for each iteration is to define a fixed variable with the options that don't change, e.g.,

palmopts = {'-i','data/4D_1.nii','-m','data/mask_1.nii','-d','data/designmatrix_1.csv','-data/contrasts_1.csv','-n',10000,'-T','-corrcon'};

Then add other options:

palm(palmopts{:},'-o','results');

Hope this helps.

All the best,

Anderson

On 4 September 2016 at 15:12, David Hofmann <[log in to unmask]> wrote:

Hi all,

I want to use PALM for analysing several (hundred) data sets, thus I need to somehow automatise it and use it in a loop. I tried to use PALM in Matlab with the function syntax instead of the command syntax so I can loop through the different nifti files, masks etc. But I'm having difficulties making this work.

Command syntax for first 4D file works:

palm -i data/4D_1.nii...    
    -m data/mask_1.nii...
    -d data/designmatrix_1.csv -t data/contrasts_1.csv -n 10000 -T...
    -corrcon -o data

but it is not possible to replace the commands/filenames by variables. 

I tried the following function syntax:

 

palm('-i data/4D_1.nii',' -m data/mask_1.nii','-d data/designmatrix_1.csv','-data/contrasts_1.csv',...
   '-n 10000','-T','-corrcon','-o data');

But I get the following error message:

Error using palm_takeargs (line 1133)
Unknown option: "data/4D_1.nii"
Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});
Error in palm (line 81)
palm_core(varargin{:}); 

Any help appreciated!

greetings

David