Clarification on FreeSurfer Outputs from Longitudinal fMRIPrep Processing with --longitudinal Flag

[mahta.karimpoor]

Dear Neurostars Team,

I hope this message finds you well.

I am currently working on longitudinal fMRI data and using fMRIPrep with the --longitudinal flag enabled to ensure proper processing across multiple sessions per subject. I understand that this flag triggers longitudinal FreeSurfer processing and generates an unbiased within-subject T1 template. However, I am a bit unclear about the expected output structure, particularly how the FreeSurfer outputs and fMRIPrep’s anatomical derivatives are organized in this context.

Specifically, I would appreciate clarification on the following:

1. FreeSurfer Directory Structure:
   Should I expect to see a .long.subjectID_base directory for each session within the subject’s FreeSurfer directory?

2. fMRIPrep’s anat Folder:
   Is the anat folder generated outside of session-specific folders in the output derivatives/fmriprep/subjectID directory intended to represent the unbiased template space created by FreeSurfer? Below is how I see the directory structure:

sub-Teen01:
anat
figures
log
ses-01
ses-02

3. Reference Space for Functional Registration:
   When using the --longitudinal option, is the functional-to-anatomical registration in the final fMRIPrep output for each session performed using the session’s .long FreeSurfer reconstructions, considering the unbiased base template?

I want to ensure I’m correctly interpreting and using the longitudinal outputs, especially for downstream analyses that assume a consistent anatomical reference space across timepoints.

Thank you in advance for your time and help in clarifying this.

Best regards,

Mahta

[Steven]

Hi @mahta.karimpoor

@mahta.karimpoor

I understand that this flag triggers longitudinal FreeSurfer processing

Not quite. It creates an unbiased T1w template from all available T1w images (instead of aligning everything to first image) that FreeSurfer is run on. That is different than longitudinal freesurfer.

@mahta.karimpoor

Is the anat folder generated outside of session-specific folders in the output derivatives/fmriprep/subjectID directory intended to represent the unbiased template space created by FreeSurfer?

Not created by FreeSurfer longitudinal stream, as explained above. But yes, it represents the unbiased template that is used for all sessions.

@mahta.karimpoor

3. When using the --longitudinal option, is the functional-to-anatomical registration in the final fMRIPrep output for each session performed using the session’s .long FreeSurfer reconstructions, considering the unbiased base template?

Not .long from FreeSurfer, but yes it is from BOLD to the anatomical template, however it is defined.

You can run run special freesurfer processes (e.g., longitudinal freesurfer or fastsurfer) outside of fmriprep, as normal, and then import that with the --fs-no-resume flag.

Best,
Steven