Hi,

After you have imported your structural and functional files into Conn, you can then include the six motion parameters as a text file into Conn. This would essentially be a text file with six columns corresponding to the three translation parameters and three rotation parameters. The number of rows would be the same as the number of scans that you have (number of volumes). Typically, SPM style motion parameter file contains translation parameters in mm and rotations in radians. There is a chance that Conn can read other types of motion parameter file but I haven't tested that.

As far as scrubbing parameters go, you can simply run the "functional Outlier detection (ART-based identification of outlier scans for scrubbing)" step from the preprocessing menu. Do note that in the default preprocessing pipeline, this step is run immediately after realignment (and slice timing correction if you have done that). If you have already detected outliers using other approaches (such as DVARS/FD/FSL's motion outliers), you could include them as "scrubbing" as a first level covariate. This is typically a .mat file with a variable named "R" containing a matrix of 1's and 0's with each column having a single value of 1 for the volume that has been marked as outlier and everything else in that column as zero. This is similar to the output from FSL's motion outliers. This is the format for the art_regression_outliers*.mat file.

Finally, as far as I can make out, the QC_timeseries variable in the first level contains standardized values (z scores) of global signal and motion parameters (though I am not 100% sure about this part).

As an alternate, type "art" on the MATLAB command prompt to launch the ART GUI.


Hope this helps


P.S: If you are importing FreeSurfer data into Conn, you might want to change some of the preprocessing options


Best
Pravesh

Originally posted by Masaki Yoneta: