help > RE: Is it possible to skip some CONN preprocessing steps
Dec 6, 2018  07:12 AM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Is it possible to skip some CONN preprocessing steps

Yes, it is possible to skip certain preprocessing steps and also to apply custom preprocessing pipeline. Further, it is also possible to attempt to continue analysis steps from a point where the execution failed (in certain places). For example, you could try going to preproessing step and deselect "process all subjects" and select the subjects for which the steps have failed.

Specifically in your case, if you have used the default volumetric pipeline (direct normalization to MNI space), then step 6 is structural segmentation and normalization. This step is preceded by structural centering. If these are the steps in your case, you should be able to run them separately without any issue (I would suggest running both: centering and segmentation/normalization step). When it comes to step 7, just check the functional data in your setup tab. If it shows normalized functional data (wau* or wu*.nii file), you can run smoothing without any problem (which is step 7). However, if it shows the raw functional files in the Setup tab, you would have to load the normalized functional files into Conn before proceeding further.

Do take care of having sufficient memory before proceeding further. Depending on your choices, Conn may end up taking quite a bit of hard disk space!

Hope this helps


Originally posted by madeleine:

I've been running one of the default preprocessing pipelines in CONN from the GUI but it crashed on step 6/7 due to a full disk issue. Is it possible to get CONN to skip the first 5 steps and continue on from step 6? Or is that not advisable?

Thanks so much for any advice you can give!

Kind regards,


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madeleine Dec 6, 2018
RE: Is it possible to skip some CONN preprocessing steps
Pravesh Parekh Dec 6, 2018