Dear All

Is the information which slice order was used somewhere to find in conn (in a fully processes pipeline, with preprocessing done in conn)?

Greetings,
Lucas

PS: I apologise for frequent questions recently.

Dear Lucas,

Please don't apologize for asking questions on a forum, that's the purpose :-)

I don't think CONN stores the slice order information anywhere, because anyway the user should provide the information (otherwise CONN has no way to derive automatically the slice information in a reliable way, see the SPM wikibook on Slice Timing for more info). If you did not provide the slice order info during the preprocessing, then I guess CONN skipped the slice timing correction, which is usually fine if your TR <= 2 seconds.

Hope this helps,
Stephen

Dear Lucas&Stephen,

If you are using a somewhat recent version of CONN there is an undocumented log there that keeps track of all of the preprocessing steps run on your project. You can access that log using the syntax:

   Log = conn('get','SetupPreproc.log');     % all entries
   LogEntry = Log{end};                          % last entry only

Then simply look at the variable LogEntry which will contain the last preprocessing steps run on your data, the 3rd element in that cell array will be the list of preprocessing steps, and the 13th element (the one after the field 'sliceorder') will contain the sliceorder that you used there. 

Hope this helps
Alfonso
Originally posted by Stephen L.:

Dear Alfonso,

Thank you very much for the info, it's very useful to know that CONN is logging everything :-) I think this could be added to the manual :-)

Best regards,
Stephen

Thank you! This is very helpful.

Greetings,
Lucas

Dear Alfonso,

a follow-up question: is 15.h recent enough for the log? I doesn`t seem to work there. Preprocessing was done with that version, ,ay it be that tha slice order is saved somewhere else still?

Thank you,
Lucas