Dear Ben,
It sounds like you are attempting to run a higher-level analysis if you are seeing a "Select FEAT directory" dialogue box. If you want to run a first-level analysis then the input should be "Select 4D data". And if you have already pre-processed some data then you just enter the pre-processed 4D data here and turn off appropriate settings in the "Pre-stats" tab. You shouldn't need to do anything else.
Also (guessing from your subject title) if you want to enter previously calculated motion parameters and not run motion correction again on the pre-processed data (and I would not run motion correction again) then instead of using the "Motion Parameters" drop-down on the Stats tab, you should add the motion parameter via the "Select confound EVs text file(s)", or alternatively just enter them directly into the GLM in the model setup. Either way it will add the motion parameters for you in the GLM.
Hope this helps.
All the best,
Mark
> On 7 Mar 2018, at 14:58, Ben Gold <[log in to unmask]> wrote:
>
> Hi experts,
>
> I'd like to run a few different first-level analyses on some preprocessed data, and I'd like to include the motion parameters estimated with MCFLIRT as confound EVs. But I'm having a bit of trouble setting it up.
>
> I created a new directory for my analysis (i.e., separate from the one with the preprocessed data), and copied the filtered_func_data.nii.gz from the preprocessing directory into this one. After an error message at the "Select FEAT directory" dialogue, I also copied over the design.fsf file from the preprocessing directory to the new one. And after an error in my logfile saying that it couldn't find the absbrainthresh.txt file, I copied that over, too.
>
> Now I'm getting another error in the logfile, this time saying:
> /usr/share/fsl/5.0/bin/smoothest -d 1400 -m mask -r stats/res4d > stats/smoothness
> Image Exception : #22 :: ERROR: Could not open image mask
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted (core dumped)
>
> Yet the analysis also created my pe, cope, tstat, varcope, and zstat images. So I'm not sure if this is something to worry about or not. Should I also copy over some mask from the preprocessing directory? If so, what is it? And should I also copy the /mc/ folder of the preprocessed data directory with the MCFLIRT information? Am I even right to copy all these things over, since I can't find any instructions about this in the user guide or anywhere else for that matter?
>
> Thank you for the help!
>
> --
> Ben Gold
> Doctoral Candidate
> Integrated Program in Neuroscience
> Montreal Neurological Institute
> McGill University, Canada
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