I have a dataset that has been preprocessed using fmriprep 1.5.1rc1 as recommended in this thread, however, I’m running into an issue where my preprocessed data seem to be on different grids. I have many subjects (20), sessions (151), tasks, and runs (226) and I cannot find a pattern as to which runs are on which grid size.
All the data were acquired on a 96 x 96 x 31 grid with a voxel size of 2.083 x 2.083 x 4.4mm.
It seems as though I have 2 possible output grids, and, while the dimensions are different, it seems like the voxel sizes were preserved in some way.
88 x 51 x 88 with a voxel size of 2.083 x 4.400 x 2.083 or
88 x 106 x 43 with a voxel size of 2.083 x 2.083 x 4.400.
I have not systematically analyzed all grids for all runs, but I’m working on that now. It does seem like the latter output size is more common than the former. Does anyone have ideas as to why these output grids are different, though? Shouldn’t all output grids be the same if the input grids are identical?
A couple other points:
- All of the runs within a session seem to be on the same grid
- However, sometimes not all sessions per subject are on the same grid
- I’m using
Here is the fmriprep command I used:
export TMPDIR=/lscratch/$SLURM_JOB_ID && export SINGULARITY_BINDPATH=/gs3,/gs4,/gs5,/gs6,/gs7,/gs8,/gs9,/gs10,/gs11,/spin1,/scratch,/fdb,/data,/lscratch && export SINGULARITYENV_TEMPLATEFLOW_HOME=/home/fmriprep/.cache/templateflow && mkdir -p $TMPDIR/wrk/sub-P03 && singularity run --cleanenv -B /home/dmoracze/.cache:/home/fmriprep/.cache /data/DSST/containers/fmriprep-1.5.0.simg /data/dmoracze/rawdata /data/DSST/KRNS/bids/derivatives/fmriprep-1.5.0 participant --participant_label sub-P03 -w /lscratch/$SLURM_JOB_ID/wrk/sub-P03 --nthreads 12 --omp-nthreads 8 --mem_mb 30 --fs-license-file /home/dmoracze/license.txt --output-spaces func fsaverage6 MNI152NLin6Asym --use-aroma --error-on-aroma-warnings