diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..1cd4cac --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..c59e047 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 diff --git a/README.md b/README.md index 60899da..7b52028 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ sub\-XXXX\_ses\-Y\_task\-{rest, other\_task\_name}\_run\-ZZ\_desc\-confounds\_ti (or specifically, for example: sub\-BB06601\_ses\-1\_task\-rest\_run\-02\_desc\-confounds\_timeseries.tsv) -While this *confound* file contains a large number of metrics, we have specific interest in sumarising the following metrics: +While this *confound* file contains a large number of metrics, we have specific interest in summarising the following metrics: * Estimated **head-motion parameters** - the 6 rigid-body motion parameters (3 translations and 3 rotation), estimated relative to a reference image: @@ -40,7 +40,7 @@ While this *confound* file contains a large number of metrics, we have specific * global_signal - the average signal within the brain mask. -* **Count of motion outliers** - Scans occuring at times of particularly high motion are flagged by the motion\_outlierXX column. For summary, we want the count of 'motion_outliers' (or equally, the largest XX). +* **Count of motion outliers** - Scans occurring at times of particularly high motion are flagged by the motion\_outlierXX column. For summary, we want the count of 'motion_outliers' (or equally, the largest XX). ### The Summariser Tool Given a pointer to a nibabies result directory, find each functional run, and create a table that aggregates the following content: diff --git a/SumarizeNibabies.sh b/SumarizeNibabies.sh index 8e83adb..777fda3 100755 --- a/SumarizeNibabies.sh +++ b/SumarizeNibabies.sh @@ -15,7 +15,7 @@ outpt_file=$2 echo "Processing the $inpt_dir for nibabies summarization and writing the output to $outpt_file" -# Check for existance of input directory +# Check for existence of input directory if [ -d $inpt_dir ]; then echo 'Input Directory exists, let us forge ahead' else @@ -23,7 +23,7 @@ else exit 20 fi -# Check for nonexistance of output file +# Check for nonexistence of output file if [ -f $outpt_file ]; then echo 'Output file exists, let us stop' exit 30 @@ -190,7 +190,7 @@ for f in ` find ${inpt_dir} -iname "*confounds_timeseries.tsv" ` ; do done # Display number of results proessed -echo "We pocessed $COUNTER files, hooray!" +echo "We processed $COUNTER files, hooray!"