QSIPrep: Is it possible to manually specify TOPUP images?

Software Support
1

Summary of what happened:

From the citation boilerplate

“A total of 2 distortion groups were included in the data data. Distortion group ‘0 1 0 0.063080’ was represented by image 1 from sub-698_acq-b700_dir-PA_dwi.nii.gz. Distortion group ‘0 -1 0 0.063080’ was represented by image 7 from sub-698_acq-b700_dir-AP_epi.nii.gz.”

I understand from the documentation that the algorithm performs a calculation similar to the developmental HCP pipelines based on pairwise spatial correlations, but I was wondering whether it was possible to tell qsiprep which images to use for TOPUP? For example, I would like to use the image 1 (first image attached) to TOPUP instead of image 7 (second image attached), would that be possible?

When I examined the confounds tsv file (in /qsiprep/<subID>/dwi/), I also could not see a “selected_for_topup” column, so I was wondering if there was another confounds tsv file I was not locating.

(The column headers I have are: framewise_displacement, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z, eddy_stdevs, original_file, grad_x, grad_y, grad_z, bval, image_mean, series_b0_mean, series_b0_correction, DWIDenoise_pre, DWIDenoise_post, DWIDenoise_change)

Command used (and if a helper script was used, a link to the helper script or the command generated):

export APPTAINERENV_FS_LICENSE=$GROUP_HOME/freesurferlicense.txt
singularity run -e --containall --writable-tmpfs --cleanenv \
/home/groups/jyeatman/software/singularity_images/qsiprep-0.20.0.sif \
/scratch/groups/jyeatman/howard/DBP3/bidsfull \
/scratch/groups/jyeatman/howard/DBP3/qsiprepfull participant --participant-label sub-$SLURM_ARRAY_TASK_ID \
-w /scratch/groups/jyeatman/howard/DBP3/qsiprepfull-work \
--nthreads 10 \
--omp-nthreads 8 \
--output-resolution 1.2 \
--infant \
--pepolar-method TOPUP+DRBUDDI

Version:

qsiprep-0.20.0.sif

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

-

Relevant log outputs (up to 20 lines):

-

Screenshots / relevant information:

image
image1856×1606 124 KB

image
image1852×1604 114 KB

2

Hi Howard, it looks like a b>0 image is getting picked from both of these. You definitely don’t want these being used for TOPUP. Are you including bvals and bvecs for your epi fmaps? This is a case where it would be very useful.

(related to [DWI] Allow bval and bvec for PEPOLAR fieldmaps · Issue #1724 · bids-standard/bids-specification · GitHub).

3

Hi @chiuhoward,

An alternative in the meantime would be to use a tool like fslsplit to get only the volume you want out of your fieldmap file, and keep that in the fmap folder with a BIDS-valid name, and use a --bids-filter-file to ignore the full fieldmap file.

Best,
Steven

4

Hi Matt,

If I am understanding the GitHub link you posted, I would include the original bval and bvec files and rename them

/bids/<subID>/fmap/<subID>_acq-b700_dir-AP_epi.bval and /bids/<subID>/fmap/<subID>_acq-b700_dir-AP_epi.bvec respectively?

Then I’d make sure that these filenames appear in .bidsignore and rerun my qsiprep script? (in which case I should expect that TOPUP can pick up these bval and bvec files when performing the spatial correlation calculations?)

I’m also unsure why the fmaps turned out like this - the bval files look ok [0 0 700 700 700 700 700 700] and the bvec files looks like this

image

Thanks!

P.S. I also just saw Steven’s reply, will try that to get the first volume in case the other workaround doesn’t work.

5

Your solution with .bidsignore will also work. We use that for most of our datasets.

6

Thanks @mattcieslak and @Steven, including bval and bvec for the fmap with .bidsignore helps TOPUP to automatically select a “better” image!