fmriprep: [mcflirt related behaviour] Wrong motion parameters estimates in confounds_timeseries.tsv (lot of zeros!)

What version of fMRIPrep are you using?

FMRIPREP v 20.2.1

What kind of installation are you using? Containers (Singularity, Docker), or “bare-metal”?

Singularity installation (version 2.6.1-dist), running on a high performance computing cluster.

What is the exact command-line you used?

singularity run -B /scratch/jsein/BIDS:/work,$HOME/.templateflow:/opt/templateflow --cleanenv /scratch/jsein/my_images/fmriprep-20.2.1.simg \
		 --fs-license-file /work/freesurfer/license.txt /work/$study /work/$study/derivatives \
		 participant --participant-label $list_sub \
		 -w /work/temp_data_${study}\
		  --mem-mb 50000 --omp-nthreads 10 --nthreads 12 --ignore slicetiming --fd-spike-threshold 0.5  \
		  --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym --return-all-components --cifti-output 91k 

Have you checked that your inputs are BIDS valid?

yes the input passes the bids-validator

Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?

Yes the visual report was generated, no error reported, it is under the dropbox link at the end of this post.

Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?

no error reported

Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?

No

fMRIPrep log

If you have access to the output logged by fMRIPrep, please make sure to attach it as a text file to this issue.

We observed this strange output while building the GLM with nuisance regressors and noting that the columns with zeros where correlated with each other.

output: HTML reports, output and confounds_timeseries.tsv files under the following link: https://www.dropbox.com/sh/3e455qbh8anqwl3/AAACn2-tnmRBhXx44M_vO0qEa?dl=0

Here is for example the content of the .par file output of mcflirt run by fmriprep: the zeros are very strange and it is a very different result from what I obtain if I use SPM for realigning the same run (but realignment is to the first scan instead to the sbref as it is set with fmriprep) No zeros are found with SPM. EDIT: I just check with my local FSL installation and I found that mcflirt is giving the same output as fmriprep! Thus it is not seem to be a problem with fmriprep, rather a strange behaviour of mcflirt! This subject had very low movements. Thank you for sharing your thoughts!

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6.30042e-05  -0  0  2.83079e-09  -0.0026651  0.0452635  
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0.000125741  -0  0  2.83079e-09  -0.00412512  0.0484292  
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0.000271837  -0  0  -1.80617e-09  -0.00468443  0.0380728  
0.000268027  -0  0  1.17999e-08  -0.00618964  0.0445663  
0.000261084  -0  0  1.35479e-08  -0.00598816  0.0452548  
0.000181061  -0  0  2.32531e-09  -0.00862791  0.0828628  
0.00036988  -0  0  2.32531e-09  -0.0119828  0.0501614  
0.00027085  -0  0  1.25974e-08  -0.00556844  0.0679252  
0.000181061  -0  0  2.32531e-09  -0.0060663  0.0913342  
0.000276382  -0  0  -2.61899e-09  -0.0119468  0.0343135  
0.000274122  -0  0  2.32531e-09  -0.00934721  0.0487565  
0.000322834  -0  0  1.18787e-08  -0.0061962  0.0650543  
0.000181061  -0  0  2.32531e-09  -0.00699194  0.0828496  
0.000181061  -0  0  2.32531e-09  -0.00716909  0.0417544  
0.000339541  -0  0  -5.74701e-09  -0.00958281  0.0612099  
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0.000181061  -0  0  2.32531e-09  -0.00365363  0.0208984  
0.000288511  -0  0  2.32531e-09  -0.0119517  0.0223716  
0.00027053  -0  0  6.85316e-09  -0.00629294  0.0500681  
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0.000181061  -0  0  2.32531e-09  -0.00860397  0.0279844  
0.000244789  -0  0  -2.63327e-09  -0.00729157  0.0500972  
2.38631e-06  -0  0  2.32531e-09  0.00281907  0.0794415  
0.000181061  -0  0  2.32531e-09  -0.00350589  0.0501742  
0.000181061  -0  0  2.32531e-09  -0.00955198  0.0625052  
-2.97965e-06  -0  0  2.32531e-09  0.00210593  0.0949698  
0.000181061  -0  0  2.32531e-09  -0.00830979  0.043568  
0.000298899  -0  0  -5.45857e-09  -0.0119505  0.0534515  
0.000181061  -0  0  2.32531e-09  -0.00190411  0.0874287  
0.000181061  -0  0  2.32531e-09  -0.00374029  0.0634447  
0.000317519  -0  0  2.32531e-09  -0.0119585  0.0529064  
0.000181061  -0  0  2.32531e-09  -0.00312477  0.0772102  
7.06293e-05  -0  0  2.32531e-09  0.00037782  0.0733328  
0.000289854  -0  0  7.07189e-09  -0.00840966  0.0473801  
0.000331191  -0  0  -5.55191e-09  -0.0119579  0.0599957  
-0.000241041  -0  0  2.32531e-09  0.0050688  0.0806819  
0.000181061  -0  0  2.32531e-09  -0.00190411  0.0167831  
0.000181061  -0  0  2.32531e-09  -0.00844981  0.0195735  
0.000340188  -0  0  2.32531e-09  -0.0119715  0.0361546  
0.000181061  -0  0  2.32531e-09  -0.00597024  0.031775  
0.000181061  -0  0  2.32531e-09  -0.00214056  0.0480441  
0.000181061  -0  0  2.32531e-09  -0.00407231  0.015303  
0.000181061  -0  0  2.32531e-09  -0.00520885  0.0195735  
0  -0  0  0  0  0.0343214  

Here is a plot (made with FSLeyes) of the translation along x, calculated with mcflirt (.par file, 4th column, ref= sbref) and with spm (rp file, 1st column, ref=1st scan): Quite different! Another example: same run, looking at the ortation around y, calculated with mcflirt (.par file, 2nd column, ref= sbref) and with spm (rp file, 5th column, ref=1st scan):