ENH: update fsl packages for reported bug fixes

[psadil]

Changes proposed in this pull request

Closes #3373

Documentation that should be reviewed

[psadil]

FWIW, those failures look like scipy/scipy#21623 (comment)

[effigies]

Can you look up the latest FSL release and see if the other pins we have are up to date? I'd rather move them as a group, as I expect they are tested together.

[psadil]

$ mapfile -t pinned < <(grep fsl- env.yml)
version_pattern="[0-9]+\.[0-9]*"
for fsl_version in 6.0.7.8 6.0.7.9 6.0.7.10 6.0.7.11 6.0.7.12 6.0.7.13; do
    echo "checking FSL ${fsl_version}"
    manifest=$(curl https://git.fmrib.ox.ac.uk/fsl/conda/manifest/-/raw/"${fsl_version}"/fsl-release.yml\?ref_type\=tags 2>/dev/null)    
    for pin in "${pinned[@]}"; do
        package_name=$(echo "${pin}" | grep -oE "fsl-[a-z0-9]+" )
        if [[ $manifest =~ $package_name ]]; then
            manifest_version=$(echo "${manifest}" | grep -oE "${package_name} ${version_pattern}" | grep -oE "${version_pattern}")
            manifest_package_w_version=$(printf "%s=%s" "${package_name}" "${manifest_version}")
            if [[ ! "${pin}" =~ ${manifest_package_w_version} ]]; then
                printf "env has %s but FSL %s has %s\n" "${pin}" "${fsl_version}" "${manifest_package_w_version}"
            fi
        fi
    done
done

checking FSL 6.0.7.8
env has   - fsl-bet2=2111.4 but FSL 6.0.7.8 has fsl-bet2=2111.7
checking FSL 6.0.7.9
env has   - fsl-bet2=2111.4 but FSL 6.0.7.9 has fsl-bet2=2111.7
checking FSL 6.0.7.10
env has   - fsl-bet2=2111.4 but FSL 6.0.7.10 has fsl-bet2=2111.7
checking FSL 6.0.7.11
env has   - fsl-bet2=2111.4 but FSL 6.0.7.11 has fsl-bet2=2111.7
checking FSL 6.0.7.12
env has   - fsl-bet2=2111.4 but FSL 6.0.7.12 has fsl-bet2=2111.8
env has   - fsl-topup=2203.2 but FSL 6.0.7.12 has fsl-topup=2203.4
checking FSL 6.0.7.13
env has   - fsl-bet2=2111.4 but FSL 6.0.7.13 has fsl-bet2=2111.8
env has   - fsl-topup=2203.2 but FSL 6.0.7.13 has fsl-topup=2203.5

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.70%. Comparing base (3e69454) to head (69038b7).
Report is 74 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3374   +/-   ##
=======================================
  Coverage   71.70%   71.70%           
=======================================
  Files          57       57           
  Lines        4259     4259           
  Branches      640      640           
=======================================
  Hits         3054     3054           
  Misses       1090     1090           
  Partials      115      115           

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[mgxd]

Retriggered the GHA jobs - this looks good to me

[effigies]

So if I understand correctly, this just means that these lines

https://github.com/nipreps/sdcflows/blob/656a51d4a734d2d8d66550e9e317386f677801a3/sdcflows/workflows/fit/pepolar.py#L144-L145

become unnecessary?

Given that we aren't patching the TOPUP interface directly, this seems fairly safe. @mgxd Were you going to test on a dataset that has an odd number of slices?

[mgxd]

No, I don't believe so, the fix for the odd # of slices has to do with a configuration option (--subsamp). We decided against changing the configuration based on even/odd slices (see nipreps/sdcflows#217)

From my understanding this fix will only be relevant/noticed on images with tight FOVs