Preprocessing Multiple Runs Stored in Separate Files

Many studies save each run (block) of a task into its own .asc file – for example, because the EyeLink recording was stopped and restarted between runs, or because each phase of a session was exported separately. This vignette shows the recommended way to preprocess that kind of data with eyeris: loop over the files, preprocess each one independently, and let the BIDS run-<index> entity keep everything cleanly organized in your derivatives.

💡 Two different “multiple runs” situations. There are two ways multiple runs can show up, and they are handled differently:

This vignette: multiple runs, each in its own separate .asc file. You process each file with its own glassbox() → epoch() → bidsify() call.
The other case: several recording segments embedded inside a single .asc file. That is handled automatically by load_asc(block = “auto”) and a single bidsify() call – see the Complete Pipeline and Anatomy of an eyeris Object vignettes. We contrast it briefly at the end.

The one concept to know: `block` is `run`

In eyeris, the input knob is called block (the block argument to load_asc()), and the output BIDS entity is called run (the run-<index> token in your derivative filenames). They map one-to-one:

block N on input → run-0N on output

So when you set the block number for a file, you are setting its run number. “Block” is eyeris/experiment-design terminology; “run” is the BIDS acquisition entity. (There is no block entity in BIDS – a separately-acquired repetition of a task is a run.) This is why, in the workflow below, you set the run number once via load_asc(block = ...) and do not need to pass run_num to bidsify().

The pattern

Suppose participant AB01 completed three runs of an associative-memory task, each saved to its own file:

library(eyeris)

dl <- path.expand("~/Downloads")
asc_files <- file.path(dl, c(
  "sub-AB01_t1_2024-01-15_10h00.00.000.asc",
  "sub-AB01_t2_2024-01-15_10h30.00.000.asc",
  "sub-AB01_t3_2024-01-15_11h00.00.000.asc"
))
stopifnot(all(file.exists(asc_files)))

output_dir <- path.expand("~/Documents/eyeris")

for (i in seq_along(asc_files)) {
  glassbox(asc_files[i], load_asc = list(block = i), verbose = TRUE) |>
    epoch(
      events = "TST_trial-{trial}_{item}_{associate}",
      limits = c(0, 0.1),
      label  = "trialEpochs"
    ) |>
    bidsify(
      bids_dir       = output_dir,
      participant_id = "AB01",
      session_num    = "01",
      task_name      = "assocmem",
      save_raw       = TRUE,
      html_report    = TRUE,
      report_seed    = 0
    )
}

What each piece is doing:

load_asc = list(block = i) sets the run number for this file. On iteration i = 1 the file becomes block_1 → run-01, i = 2 → run-02, and so on. Passing a single numeric block also forces the entire file into one run, which is exactly what you want when one file = one run (more on this in Sanity check below).
epoch() extracts your trials. Here TST_trial-{trial}_{item}_{associate} matches each trial event and parses trial, item, and associate into columns of the epoched data frame.
bidsify() writes that run’s derivatives. participant_id, session_num, and task_name are the same on every iteration, so all three runs land in the same subject/session tree, distinguished only by their run-<index>.

ℹ️ Why is there no run_num in the bidsify() call? Because bidsify() inherits the run number from the eyeris object – i.e., from the block you set in load_asc(). Setting it again in bidsify() would be redundant. (run_num exists to relabel a single-run object – e.g. force a lone file to be saved as run-03 – and it is silently ignored for objects that already contain multiple blocks.)

The equivalent: label the run in `bidsify()` instead

Setting the run number on input with load_asc(block = i) is the form we recommend, but it is not the only one. Because each single-run file already loads as one block by default, you can leave load_asc untouched and instead label each file on output with bidsify(run_num = i) – exactly the “relabel a single-run object” use of run_num from the note above. This loop writes the same run-01, run-02, run-03 derivatives as the one before it:

library(eyeris)

dl <- path.expand("~/Downloads")
asc_files <- file.path(dl, c(
  "sub-AB01_t1_2024-01-15_10h00.00.000.asc",
  "sub-AB01_t2_2024-01-15_10h30.00.000.asc",
  "sub-AB01_t3_2024-01-15_11h00.00.000.asc"
))
stopifnot(all(file.exists(asc_files)))

output_dir <- path.expand("~/Documents/eyeris")

for (i in seq_along(asc_files)) {
  glassbox(asc_files[i], verbose = TRUE) |>
    epoch(
      events = "TST_trial-{trial}_{item}_{associate}",
      limits = c(0, 0.1),
      label  = "trialEpochs"
    ) |>
    bidsify(
      bids_dir       = output_dir,
      run_num        = i,
      participant_id = "AB01",
      session_num    = "01",
      task_name      = "assocmem",
      save_raw       = TRUE,
      html_report    = TRUE,
      report_seed    = 0
    )
}

The only two changes from the first loop are: (1) glassbox() no longer receives load_asc = list(block = i), so each file loads with its default single block; and (2) bidsify() now takes run_num = i, which relabels that block as run-01, run-02, etc. Everything else – and every output file – is the same.

⚠️ The two forms are equivalent only for genuinely single-run files. run_num relabels a file that resolves to one block; if a file happens to contain multiple embedded recording segments, run_num is ignored (and bidsify() will emit a warning when verbose = TRUE) and the runs are numbered from the embedded blocks instead. load_asc(block = i) also forces the whole file into a single run, so it doubles as a guard against accidentally-multi-segment files. If you prefer the run_num form, it is worth running the sanity check below to confirm each file really is one run.

What you get

After either loop finishes, your derivatives look like this (per-run data files shown for run-01; run-02 and run-03 follow the same pattern):

eyeris
└── derivatives
    └── sub-AB01
        └── ses-01
            ├── eye
            │   ├── sub-AB01_ses-01_task-assocmem_run-01_desc-timeseries.csv
            │   ├── sub-AB01_ses-01_task-assocmem_run-01_desc-blinks.csv
            │   ├── sub-AB01_ses-01_task-assocmem_run-01_desc-events.csv
            │   ├── sub-AB01_ses-01_task-assocmem_run-01_desc-epoch_summary.csv
            │   ├── sub-AB01_ses-01_task-assocmem_run-01_desc-preproc_pupil_epoch-trialepochs.csv
            │   ├── epoch_trialEpochs/   # per-trial confounds CSVs for run-01
            │   │   └── ...
            │   ├── sub-AB01_ses-01_task-assocmem_run-02_desc-timeseries.csv
            │   ├── ...
            │   ├── sub-AB01_ses-01_task-assocmem_run-03_desc-timeseries.csv
            │   └── ...
            ├── source
            │   ├── figures
            │   │   ├── task-assocmem_run-01
            │   │   │   └── ...
            │   │   ├── task-assocmem_run-02
            │   │   │   └── ...
            │   │   └── task-assocmem_run-03
            │   │       └── ...
            │   └── logs
            │       ├── task-assocmem_run-01_metadata.json
            │       ├── task-assocmem_run-02_metadata.json
            │       └── task-assocmem_run-03_metadata.json
            ├── sub-AB01_task-assocmem_epoch-trialEpochs_run-01.html
            ├── sub-AB01_task-assocmem_epoch-trialEpochs_run-02.html
            ├── sub-AB01_task-assocmem_epoch-trialEpochs_run-03.html
            └── sub-AB01_task-assocmem.html

Every data file carries its run-<index>, and the top-level sub-AB01_task-assocmem.html report aggregates all three runs. For a full breakdown of what each derivative file contains, see the Extracting Data Epochs and Exporting Pupil Data vignette.

💡 Note on the epoch label in filenames. Epoch labels are sanitized (lower-cased, punctuation removed, digits dropped) on their way to disk, so the label = “trialEpochs” you supply appears as epoch-trialepochs in the CSV filename. If you search your output by filename, search case-insensitively.

Handling missing or non-sequential runs

A common, important question:

“What if I have runs 1–3 but run 2 was never collected? Would run 3 get saved as run 2?”

No – eyeris never renumbers your runs. The run number written to disk is exactly the number you assign via block =. There is no global counter that re-sequences runs across files.

The one thing to watch is where you get the number from. In the loop above, block = i uses the loop position, which equals the true run number only if your files really are runs 1, 2, 3, … in order with none missing. If run 2 was never collected and you only have files for runs 1 and 3, then seq_along() would hand file #2 (the run-3 file) the index 2 and mislabel it as run-02.

The fix is to drive the run number from the true run identity, not the loop position. Two robust options:

Option A – an explicit vector of run numbers, paired with your files:

asc_files <- file.path(dl, c(
  "sub-AB01_t1_2024-01-15_10h00.00.000.asc", # run 1
  "sub-AB01_t3_2024-01-15_11h00.00.000.asc"  # run 3 (run 2 not collected)
))
run_nums <- c(1, 3) # the TRUE run numbers, in the same order as `asc_files`

for (i in seq_along(asc_files)) {
  glassbox(asc_files[i], load_asc = list(block = run_nums[i]), verbose = TRUE) |>
    epoch(
      events = "TST_trial-{trial}_{item}_{associate}",
      limits = c(0, 0.1),
      label  = "trialEpochs"
    ) |>
    bidsify(
      bids_dir       = output_dir,
      participant_id = "AB01",
      session_num    = "01",
      task_name      = "assocmem",
      save_raw       = TRUE,
      html_report    = TRUE,
      report_seed    = 0
    )
}

Option B – parse the run number out of the filename. Here the run is encoded as _t1_, _t2_, _t3_, so a small regex recovers it (and naturally handles gaps, since a missing run simply has no file):

for (f in asc_files) {
  run_n <- as.integer(sub(".*_t(\\d+)_.*", "\\1", basename(f)))

  glassbox(f, load_asc = list(block = run_n), verbose = TRUE) |>
    epoch(
      events = "TST_trial-{trial}_{item}_{associate}",
      limits = c(0, 0.1),
      label  = "trialEpochs"
    ) |>
    bidsify(
      bids_dir       = output_dir,
      participant_id = "AB01",
      session_num    = "01",
      task_name      = "assocmem",
      save_raw       = TRUE,
      html_report    = TRUE,
      report_seed    = 0
    )
}

With either approach, run 3 is saved as run-03 and the gap is preserved.

ℹ️ Gaps are valid BIDS. The BIDS specification does not require run indices to be consecutive – a dataset with run-01 and run-03 but no run-02 is perfectly valid, and it faithfully records what you actually collected. So there is no need to “compress” your run numbers to fill a gap.

Fixing or re-running a single run

Because every run is preprocessed by its own bidsify() call, you can fix or re-run just one run later without touching the others – which is the main practical advantage of the separate-file workflow. For example, if you tweak a preprocessing parameter for run 2:

glassbox(asc_files[2], load_asc = list(block = 2), verbose = TRUE) |>
  epoch(
    events = "TST_trial-{trial}_{item}_{associate}",
    limits = c(0, 0.1),
    label  = "trialEpochs"
  ) |>
  bidsify(
    bids_dir       = output_dir,
    participant_id = "AB01",
    session_num    = "01",
    task_name      = "assocmem",
    save_raw       = TRUE,
    html_report    = TRUE,
    report_seed    = 0
  )

bidsify() cleans out the existing derivatives for that specific subject + session + task + run before writing, so re-running run-02 replaces only run-02’s files and leaves run-01 and run-03 untouched.

Sanity check: confirm one run per file

EyeLink .asc files sometimes contain more than one recording segment (for instance, when the tracker was stopped and restarted for a recalibration or drift correct). If eyeris auto-detects multiple segments in a file, it treats that file as multi-block – and in that case run_num is ignored and the runs are numbered from the embedded block numbers instead of from your block = i.

Passing a single numeric block (as we do above) forces the whole file into one run, which is what you want for one-file-per-run data. You can confirm a file resolves to exactly one run by checking the length of $timeseries:

library(eyeris)
#> 
#> eyeris v3.2.0.9006 - Lumpy Space Princess ꒰•ᴗ•｡꒱۶
#> Welcome! Type ?`eyeris` to get started.

# the bundled demo file stands in for one of your per-run .asc files
demo_file <- eyelink_asc_demo_dataset()

eye <- glassbox(demo_file, load_asc = list(block = 1), verbose = FALSE)

length(eye$timeseries) # 1 -> exactly one run in this file
#> [1] 1
names(eye$timeseries)  # "block_1" -> will be written as run-01
#> [1] "block_1"

If length(eye$timeseries) comes back greater than 1 for a file you expected to be a single run, that file is being split into multiple blocks; forcing block = <run number> (a single numeric, as above) collapses it back into one run.

The other case: multiple runs inside one file

If instead all of your runs were recorded into a single continuous .asc file, you don’t loop – you let eyeris split the embedded segments for you and write them in one bidsify() call:

glassbox(one_file_with_all_runs, load_asc = list(block = "auto")) |>
  epoch(
    events = "TST_trial-{trial}_{item}_{associate}",
    limits = c(0, 0.1),
    label  = "trialEpochs"
  ) |>
  bidsify(
    bids_dir       = output_dir,
    participant_id = "AB01",
    session_num    = "01",
    task_name      = "assocmem"
  )

Here block = "auto" (the default) detects each recording segment and numbers them run-01, run-02, … from their embedded block numbers.¹ See the Complete Pipeline and Anatomy of an eyeris Object vignettes for more on that path.

✨ Summary

When each run lives in its own .asc file, loop over the files and give each one its own glassbox() → epoch() → bidsify() call.
In eyeris, block is run: set the run number once via load_asc(block = ...); bidsify() inherits it, so you don’t pass run_num.
eyeris never renumbers runs – drive the block number from the true run identity (an explicit vector or a filename parse), not the loop position, and missing runs leave valid, faithful gaps (e.g. run-01, run-03).
Each run is processed independently, so you can re-run a single run later without disturbing the others.
Use length(eye$timeseries) to confirm a file resolves to a single run; pass a numeric block to force it.

📚 Citing `eyeris`

If you use the eyeris package in your research, please cite it!

Run the following in R to get the citation:

citation("eyeris")
#> To cite package 'eyeris' in publications use:
#> 
#>   Schwartz ST, Yang H, Xue AM, He M (2025). "eyeris: A flexible,
#>   extensible, and reproducible pupillometry preprocessing framework in
#>   R." _bioRxiv_, 1-37. doi:10.1101/2025.06.01.657312
#>   <https://doi.org/10.1101/2025.06.01.657312>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {eyeris: A flexible, extensible, and reproducible pupillometry preprocessing framework in R},
#>     author = {Shawn T Schwartz and Haopei Yang and Alice M Xue and Mingjian He},
#>     journal = {bioRxiv},
#>     year = {2025},
#>     pages = {1--37},
#>     doi = {10.1101/2025.06.01.657312},
#>   }

The one concept to know: block is run