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synthSR dwi-t1 reg, motioncorr, new test datasets #53

Merged
merged 10 commits into from
Mar 9, 2023
Merged

synthSR dwi-t1 reg, motioncorr, new test datasets #53

merged 10 commits into from
Mar 9, 2023

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akhanf
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@akhanf akhanf commented Feb 28, 2023

Another fairly large PR --

  • adds synthSR to images used for T1 to dwi registration
  • ensures motion-correction (moco) is used before b0s are averaged at any point in the workflow
    • moco rules moved to motioncorr.smk
  • apply topup only on b0s (we were previously applying to whole dwi, then pulling out b0s) so this is just for efficiency and to ensure we use the moco'd b0s
  • added new test datasets with only 14 dirs (and a single b0 in each scan) to test this edge case (they conveniently run faster than the previous test data too)
    • one for topup (LR+RL scan), and one for synthsrsdc workflows (single AP scan)
    • added DAGS for these

@akhanf
add moco to avg b0s before topup, and use synthsr for dwi-t1 reg
45949c4 
WIP
@akhanf
added moco for b0s within the dwi scan
529484f
@akhanf
added new *real, downsampled* test dataset with 13+1b0 directions
6046ad7 
- for testing moco workflows with edge case of having only a single b0
in each scan
@akhanf
renamed test data, added test dataset with single scan
8a5552c
@akhanf
apply_topup to b0s instead of full dwi
83e21a4 
since we were extracting the b0s anyways, and this allows
motion-corrected data to be used
@akhanf
moved moco rules to separate motioncorr.smk
c96e075 
- now have 3 separate rules, for 4d b0s before concat, 4d b0s after concat,
and 3d vols
@akhanf
added dag vis, and updated default bids to use smaller 14vol data
a275728
@akhanf akhanf marked this pull request as ready for review February 28, 2023 00:48
@akhanf
bugfix: missing snakemake.
7d73b9f
@akhanf
add consistent checks for pe_dir and eff echo sp
797cc82 
- ideally should remove this redundant code, and have the
  check_subj_dwi_metadata script do it, and write it to workflowopts
  where downstream rules can read it..
@akhanf
linting and fix typo
d96a4aa
@akhanf akhanf merged commit ff7f2fd into master Mar 9, 2023
@akhanf akhanf deleted the synthsr-reg-dwi-t1 branch March 9, 2023 17:57
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@akhanf