Hi Kevin,

You can have a look at the graph of dependencies using the command PSOM_VISU_DEPENDENCIES

You need to generate the pipeline structure first :

>> opt.flag_test = true;
>> pipeline = niak_fmri_preprocess(files_in,opt)
>> psom_visu_dependencies(pipeline)

However, for your problem I think there is a simpler solution. Change the initial transformation of the anat2func job :

>> pipeline.anat2func_subject1.files_in.transformation_init = '/path_data/my_transf_stereolin2func.xfm';

There is a flag to invert this transformation, which by default is true and you may want to turn false :

>> pipeline.anat2func_subject1.opt.flag_invert_transf_init = true;

If the initial transform is good, the algo should converge in the right place. Also, please be aware that this transformation needs to go from the T1 image *in stereotaxic space* (after linear transform) to the functional native space. 

Have a nice data preprocessing,

Pierre