Hi Dr. Spielberg,

Thank you for developing this tool! 

I'm having some difficult at the preprocessing stage. First, when I hit the "Start" button on the GTG_preprocess_GUI, a Finder window pops up with my subject directory. The parallel pool won't run until I hit cancel in this window. After I've done this, the pool will run for about 5 minutes, and then I receive this error message:

Error using dlmread (line 54)
Filename must be a string.

Error in preprocessGTG_run_processing_subfunc (line 463)
mot_pred = dlmread(par_filename);

Does this have anything to do with my directory set-up? Or is it related to motion-correction? The 4D files that I am inputting have already been motion-corrected using MCFLIRT, so I don't select that option in the GUI.

Please let me know if you have any thoughts!

Thank you so much!

Shaadee

Hi Shaadee,

It sounds like you're asking for the motion parameters to be partialed out, but not doing the motion correction within the toolbox.  So, the toolbox needs you to supply the motion parameters, which is what that popup window is asking for (you need to navigate to the motion parameters for the first subject).  The filenames need to follow the same rules as for the MRI files (e.g., having a consistent directory structure across participants, having the subject number somewhere in the filepath, if not filename, so that the toolbox can locate the appropriate file for each participant by replacing the subject number).  

Right now, the toolbox expects a file like that output from FSL's MCFLIRT - so a text file with six columns of motion parameter data.  If you didn't do your motion correction in FSL, you'll need to put the data into that format and the file extension needs to be .par (that is something that will be made more flexible in a future version, but currently only .par works).  

So, in order to partial motion parameters you either need to do motion correction within the toolbox or supply that data via a .par file.  Let me know if you still run into problems....

Best,
Jeff

Everything ran smoothly! Thank you so much, Jeff.

Best,
Shaadee