Hi Johanna,

The preprocessing pipeline runs one step at a time through all subjects (i.e. first it runs realignment through all subjects, when that finishes correctly it runs slice-timing correction through all subjects, etc.). When the pipeline is stop, either manually or by running into an error, the CONN project will maintain the state of the last step in the pipeline which was successfuly run, so you can continue the pipeline through the next step (the one that did not complete correctly) until the end.

In your case that means you can click on the 'Run Preprocessing' button to restart your preprocessing pipeline, then select all of the steps in your current pipeline prior to "functional Slice-Timing Correction" step (the ones that alreaedy finished correctly) and click on 'Remove' to remove those steps from the pipeline, and then click on 'Start' to have the preprocessing pipeline continue where it left off.

Hope this helps

Alfonso

Originally posted by shivapriya25:

Hi,

I've just run into a problem concerning slice timing in one subject during preprocessing, so I had to stop the pipeline and troubleshoot first. Now I've seen that apparently, preprocessing has not run through in all subjects, and the last step seems to habe generated some file named "meanuXXXX". Do I have to start from scratch or can I somehow continue where I left? (I've used the stanard pipeline)

 

Thank you so much for your help

Johanna