Works great, thank you!
2016-09-05 8:53 GMT+02:00 Anderson M. Winkler <[log in to unmask]>:
> 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
>>
>>
>>
>>
>>
>
