Intermediate Processing (--intermed)

Intermediate Processing¶

CLI flag: --intermed task1,task2,...

Intermed tasks perform intermediate MRI processing steps (e.g. structural normalization) that staged pipelines depend on. Multiple intermed tasks can be requested in one run — they execute in parallel after recon, and staged tasks wait for all of them.

[recon]
     |
     +-- [volume]  ─┐  (parallel)
     +-- [bfc]    ──┤
                    |
              [cards_preprocess]   (waits for ALL)
              [kidvid_preprocess]

volume¶

What it does: Skull stripping and nonlinear registration to template using AFNI’s @SSwarper. Produces anatomical warp files used by downstream AFNI task fMRI pipelines.

Tool: AFNI (@SSwarper, 3dQwarp)
SLURM profile: standard_short (32 GB, 8 h) — array job
Script: sswarp_scratch.sh
Depends on: recon
Input: {output}/BIDS/sub-{subject}/ses-{session}/anat/
Output: {output}/AFNI_derivatives/sub-{subject}/

Config entry:

tasks:
  volume:
    environ: ["afni_24.3.06"]
    template: "HaskinsPeds_NL_template1.0_SSW.nii"

The template field becomes $TEMPLATE in the wrapper script, accessible inside sswarp_scratch.sh.

bfc¶

What it does: Estimates B0 field maps for susceptibility distortion correction (SDC) using SDCFlows. Produces fieldmap derivatives used by downstream fMRI pipelines.

Tool: SDCFlows (via Singularity)
SLURM profile: standard_short (32 GB, 8 h) — array job
Script: sdcflows.sh
Depends on: recon
Input: {output}/BIDS/
Output: {output}/BIDS_derivatives/sdcflows/

Config entry:

tasks:
  bfc:
    container: "sdcflows-mriqc-2.10.0.sif"

Adding a new intermed task¶

Any task defined under the intermed: section of config.yaml can be requested via --intermed. To add one:

1. Add a script in scripts/{project}/.

2. Register in config.yaml under intermed::

   intermed:
     - name: bfc
       profile: standard_short
       array: true
       input_from: recon
       scripts: [bias_field_correction.sh]
       output_pattern: "{base_output}/AFNI_derivatives"

3. Add task parameters in your project config:

   tasks:
     bfc:
       environ: ["afni_24.3.06"]

4. Run: neuropipe run ... --intermed volume,bfc

Usage¶

# Single intermed task
neuropipe run \
  --subjects 001,002 \
  --input /data/BIDS \
  --output /data/processed \
  --work /data/work \
  --project my_study \
  --session 01 \
  --intermed volume

# Multiple intermed tasks (run in parallel)
neuropipe run ... --intermed volume,bfc

# Combined with staged pipelines
neuropipe run ... --intermed volume,bfc --staged-prep cards,kidvid