Dear Kevin,

If you want to restart the stage callled NAME_STAGE, use the following option :

opt.psom.restart = {'NAME_STAGE'};

Note that any stage that contains the string NAME_STAGE will be restarted. So :

opt.psom.restart = {'motion_Wrun_subject1_session1_run1'}

will restart only one job, while

opt.psom.restart = {'motion_Wrun_subject1'}

will restart all within-run motion correction jobs for subject 1, and

opt.psom.restart = {'motion_Wrun'}

will restart all within-run motion correction jobs for every subjects.

Just in case, I am going to explain how to use that to solve a specific issue. Say the T1-fMRI coregistration has done a really poor job, and you came up with a manual transformation. You can replace the trasnformation estimated by anat2func by overwritting the following file (found in anat/subject1/) :

transf_subject1_nativefunc_to_stereolin.xfm

Then you restart the jobs that come after the anat2func :

opt.psom.restart = {'mask_ind_stereolin_subject1','concat_transf_nl_subject1'};

Note that this trick will only work if "size_output" is all . Otherwise the pipeline is going to re-run most of the pipeline for subject1 (because the intermediate outputs have been cleaned up), including the anat2func. In this case I'd recommend to run the pipeline with the 'all' size ouptut only for subject1 in a separate folder than the rest of the subjects of the study.

In the future I want to develop simpler ways to implement semi-automated pipeline execution, but right now that's the best way to do it.

I hope this helps, 

Pierre