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PennLINC / qsiprep

Preprocessing of diffusion MRI
http://qsiprep.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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selected_for_topup missing from confounds.tsv #365

Open cookpa opened 2 years ago

cookpa commented 2 years ago

From the docs:

In versions 0.13 and later, QSIPrep finds the “most representative” b=0 images per warped group. 
A nearly identical approach is used in the developmental HCP pipelines, where a pairwise spatial correlation score is calculated between all b=0 images of the same warped group and the images with the highest average correlation to the other images are used as input to TOPUP. 
To see which images were selected, examine the selected_for_topup column in the confounds tsv file.

I don't see selected_for_topup in my confounds using 0.14.3. I tested on ABCD data but others have seen the same issue with HCP data.

Here's the command I ran

singularity run   --cleanenv   --no-home   -B /scratch/qsiprep.12624383.kphx81Om.tmpdir:/tmp   \
  -B /project/ftdc_pipeline/templateflow:/opt/templateflow   -B /appl/freesurfer-7.1.1:/freesurfer   \
  -B /project/ftdc_misc/pcook/synB0/bids:/data/input   \
  -B /project/ftdc_misc/pcook/synB0/qsiprep2:/data/output   \
  /project/ftdc_pipeline/pmacsPreps/containers/qsiprep-0.14.3.sif  \
  /data/input /data/output participant   --fs-license-file /freesurfer/license.txt   --notrack \
  --nthreads 2   --omp-nthreads 1   --work-dir /tmp   --skip_bids_validation   --stop-on-first-crash \
   --verbose   --dwi-only --participant-label sub-999999 --output-resolution 1.7
tpatpa commented 2 years ago

Hi,

I couldn't find it in the selected_for_topup column in the confounds tsv file, but I think that the TOPUP Inputs section in the ..data/derivatives/qsiprep/sub-XXXX.html can be helpful.

Tal