T1w reference for fMRI

When functional registration is enabled, the T1w reference is selected based on what data are available for the subject and on the anat.synthesis_level configuration setting (see Scenario 2.2 — T1w in multiple sessions).

Overview

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flowchart LR
    A{"Subject<br/>has T1w?"}
    A -->|No| B(["Template T1w"])
    A -->|Yes| SYNTH["<b>SYNTH</b>: multiple T1w<br/>runs per ses<br/>→ one T1w"]
    SYNTH --> D{"T1w in how<br/>many sess?"}
    D -->|one ses only| E(["That ses's T1w"])
    D -->|multiple ses| H{"anat.<br/>synthesis_level?"}
    H -->|"subject (default)"| I(["Subject-level T1w<br/><i>shared by all func ses</i>"])
    H -->|session| J(["Same-ses T1w<br/><i>or lexicographically first<br/>other ses, if absent</i>"])

    classDef result fill:#ecfdf5,stroke:#059669,color:#064e3b
    classDef proc   fill:#eff6ff,stroke:#3b82f6,color:#1e3a8a
    classDef decision fill:#eef2ff,stroke:#6366f1,color:#1e1b4b
    class A,D,H decision
    class B,E,I,J result
    class SYNTH proc

Scenario 1 — No T1w for the subject

When no T1w image exists for the subject, all functional sessions automatically use the specified template T1w.

Scenario 2 — T1w available for the subject

Note

Within-session synthesis — when a session contains more than one T1w run, they are always synthesized into a single T1w before anything else. This step is automatic and applies to all cases below.

Scenario 2.1 — T1w in only one session

Functional runs in the same session as the T1w use it directly.
Functional runs in any other session also use that session’s T1w as the anatomical reference.

Scenario 2.2 — T1w in multiple sessions

When T1w images exist across multiple sessions, the anat.synthesis_level config option controls what happens:

anat:
  synthesis_level: "subject"   # default — or "session"

``synthesis_level: “subject”`` (default)

All T1w images across sessions are combined into a single subject-level T1w. Every functional session of the subject uses this one shared T1w. This setting is suitable for cross-sectional studies where sessions for a subject are assumed to be equivalent.
``synthesis_level: “session”``

Each session retains its own T1w. Functional runs in a session that has a T1w use it directly. Functional runs in a session without a T1w fall back to the T1w from the lexicographically first other session of the same subject. This setting is suitable for longitudinal studies where each session’s T1w should be treated independently.