I have 3 questions as I work through a a second voyage of fmriprep.
We use a GE Healthcare Discovery MR750 3T MR System which does not output any slice timing information when converting to BIDS with dcm2bids. Searching the dicom headers with dicom_hdr I see no labeled field that would provide slice timing information or potentially allow for the calculation of it. I had noticed some threads where Chris Rorden commented on the topic of extracting this information after having gotten sample data from a GE scanner but am not sure what the results were. Is there a way I can get or calculate this information? Is there something specific I should be looking for? Unfortunately I think my problem is that I’m not sure what to look for as many of the rows in the dicom header are unlabeled.
I notice that fmriprep just saves the finalized .nii files. Is there a way interim functional files can be saved? My PI would like a complete record of the processing done.
In a similar vein to question 2 is there anywhere the actual fsl/afni/etc. commands that are run on the data are stored? I saw the passes to nipype on the GitHub page and it seems like the commands are shown in the terminal as they are run but having an exact list of commands outputted in a single file (or something similar) would be useful in case a particular step does not perform well and parameters need to be tweaked. This is said understanding that you have optimized the pipeline but nothing ever works uniformly for us.
I actually just thought of a 4th question. I also noticed in one of the GitHub code files that fmriprep took non-steady-state scans into account somehow? However, when I ran my first subject through fmriprep - not physically removing the pre-steady-state scans - my GS, GSCF, GSWM, and DVARS parameters all showed essentially a big spike followed by a flat line, likely reflecting the pre-steady-state data affecting these parameters. When you run data through fmriprep should the pre-steady-state scans be removed first? If so will this removal affect any of the BIDS information (i.e. number of scans?)
Thank you for an interesting and helpful tool and for your help!