Hi,
I got a bad coregistration between fmri scan and the t1 image (the both were centered). I suspected (for example) a wrong brain masking on the native fmri image. I would like to check this step. The mode 'all' doesn't keep any intermediate outputs regarding the coregistration. As recommended, I edited a file psom_gb_vars_local.m into the NIAK folder, I also defined a temporary directory. Unfortunately, its content is deleted, is it possible to skip this deletion in order to check the brain masking ?

Dear Kevin,

The major intermediate outputs should be located in the folder anat/(subject_id). There are a number of temporary files that would require to put a breakpoint in the job. If you are familiar with Matlab's debugging tools, you can have a look at the following tutorial to debug jobs:
https://github.com/SIMEXP/niak/wiki/Niak...

If you think that one particular output should be kept, let me know. For your coregistration problem, please check first that the T1 was properly aligned. You can generally solve issues by tweaking

   opt.t1_preprocess.nu_correct.arg = '-distance 75';

You can also turn on or off the centering of the fMRI volume for this particular dataset:

   opt.slice_timing.flag_center = 0;

Note that you can change this parameter for one subject only, e.g.

   % Anything that usually goes in opt can go in param.
   % What's specified in opt applies by default, but is overridden by tune.param
   opt.tune(1).subject = 'subject1';
   opt.tune(1).param.slice_timing.flag_center = true;

   opt.tune(2).subject = 'subject2';
   opt.tune(2).param.slice_timing.flag_center = false; 

I hope this helps,

Pierre

By the  way, I have added a small paragraph on the tuning of individual parameters in the documentation, as well as a link to the procedure of quality control:
http://niak.simexp-lab.org/pipe_preproce...

Best,

Pierre