Bold brain mask not correct + problem with bold signal itself

Hi all,
I have encountered some issues with bold brain masks in some of our subjects multiband, multiecho data. I processed the data using fMRIPrep version 20.1.0rc2. In total, 4 out of 41 subjects seem to have problems with the bold brain mask and one subject has problems with the EPI bold signal itself. I have gone through a lot of other similar problems on neurostars, but unfortunately I couldn’t find the solution. Also, I am new to fmriprep, so I guess that also doesn’t help. Below I described three subjects to show you the errors I ran into:

sub-1008; the brain mask calculated on the bold signal seems to go wrong, even though the bold signal itself looks fine (see screenshots on sub-1008). The output file doesn’t give any errors, but as you can see in the report the incorrect bold brain mask impacts the ICA procedure. In addition, a confounds file is made but it seems incomplete.

sub-1025: I think the problem is similar to sub-1008, though this time there is no brain mask on the bold signal at all (or so tiny that a confounds file was not be made, this is also reflected by the lack of summary in the report). Though this time an error was given (can be seen in report)

sub-1013: this problem is different. It looks like there is something wrong with the axes. The bold brain mask looks correct, however this time the bold signal itself looks weird. (See both screenshots on sub-1013). Again, no errors were given in the output files. This error was only found in the session 1, session 2 looks good.

A few notes:

  • I re-ran the subjects that contained errors, one time with ICA, one time without ICA, but this didn’t make a difference.
  • I know the version I used is flagged because of a fieldmap bug, but I don’t use distortion correction so I thought this wouldnt make a difference
  • The input nifti files I used look good
  • I included zipped files with the figures and html files for these three subjects on the drive: https://drive.google.com/drive/folders/1IzJRw9TiORyAOz6TzbXhC1wP6nhsT7eF?usp=sharing
  • In the reports you will probably see the following: * Phase-encoding (PE) direction: MISSING - Assuming Anterior-Posterior. I guess I didn’t include this in the json files, but our data is indeed A-P, so I think this shouldn’t be the problem.

Code:
function run_fmriprep() {
this_sub=$1
cmd="singularity run --cleanenv
-B "TMPDIR"/bids:/data \ -B {output_path}:/out
-B ${workdir_path}:/work
TMPDIR"/(basename ${simg}) /data /out participant
–participant-label $this_sub
-w /work
–fs-license-file /work/FS_license.txt
–nthreads 8
–verbose
–omp-nthreads 6
–mem_mb 80000
–ignore slicetiming
–output-spaces MNI152NLin6Asym T1w
–use-aroma
–fd-spike-threshold 0.5
–dvars-spike-threshold 1.5”

echo $cmd
eval $cmd

}

I hope you can help! Let me know if extra information is needed!

Best,
Fabienne

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