Hello Alfoso / CONN experts,

1) I am wondering how I can run commands for specific/a few subjects only without having to rerun the steps for the whole sample I have defined in the setup before?

2) Also how can I remove subjects completely from the pipeline/set up etc?

Up to now, I am aware that when I run something using the batch, the commands are run for all the subjects. Thus I have problems testing things in single subjects/or add a few new subjects without rerunning the whole thing (which also has the danger of messing things up maybe).


Please share your wisdom with me :)

Thank you very much,

Hi Panagiotis,

Regarding (1) if you are referring to preprocessing steps, in the preprocessing GUI you may uncheck the 'all subjects' option and simply select the subset of subjects that you would like to preprocess. If, on the other hand, you are referring to any other step in CONN (e.g. Setup/Denoising/First-level analyses), then it is even simpler, as you can simply select the option that reads 'do not overwrite (skip already processed subjects/ROIs)' when running those steps and that will automatically run only on those subjects where these steps have not been previously run.

Regarding (2), you may change the number of subjects in the Setup.Basic step and that will prompt you to select which subjects you would like to remove, and that will entirely remove those subjects from your CONN project. That said in general I recommend keeping your subjects in the CONN project for future reference and simply explicitly removing those subjects from your second-level analyses instead (e.g. using the procedure described in this post https://www.nitrc.org/forum/message.php?msg_id=34434 )

Hope this helps
Alfonso
Originally posted by Panagiotis Iliopoulos:

Thank you a lot Alfonso again :)

How can I do these using the conn batch, since I reran my processing using a batch script?

Thank you,
Panagiotis.

Hi Panagiotis

You may use the BATCH.subjects field to indicate which subject(s) you want to run, and that applies equally to all steps run in that batch command, including preprocessing/setup/denoising/1st-level analyses (see "help conn_batch" for details).

Best
Alfonso
Originally posted by Panagiotis Iliopoulos: