I promise I keep asking questions only because I love the program so much I’m just trying to figure it out. Wish I could mail you guys a fruit basket or something.
I’m so sorry but I have to ask this question because it has been KILLING me for the last 3 days. It’s for peace of mind,.
Annnnnyway, for bold-bold transform processing, my graph1.json starts out generating a reference file and then running MCFLIRT as steps 5 & 6, respectively.
I tried to replicate this code with the following in a Jupyter notebook:
gen_ref = EstimateReferenceImage(in_file = func_filename).run() mcflirt = fsl.MCFLIRT(in_file = func_filename, ref_file = gen_ref.outputs.ref_image, save_mats=True, save_plots=True).run()
In this example func_filename is my raw functional EPI run. This seemed easy enough. The masks that come out of the
gen_ref command are the same. The problem is that the parameters in the
_mcf.nii.gz.par file are not the same between the FMRIPREP file and the one I generated with the above commands.
Now this may be the dumbest of dumb questions but, should they not be the same? I know algorithmic differences come into play between softwares and even within the same command sometimes but I didn’t think MCFLIRT was one of them. Also whenever I run this Jupyter code I get the same .par file so I’m not sure what exactly I’m missing here. The input parameters to my Jupyter stuff matches the report that came out of FMRIPREP.
Can anyone illuminate this because I am dying to know.