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Description

The pipeline processes cross sectional and longitudinal data.

Specific actions performed: create models of the brain, process fMRI data, measure properties such as cortical thickness and regional volumes, align individuals based on their cortical folding patterns.

Can be run on

Freesurfer_5.3.xml pipeline is used for MR sessions with good quality T1 data such as MPRAGE.
NOTE: Freesurfer_Snapshots.xml pipeline MUST be installed for FS 5.3 to run successfully.

Project Inputs

Name
Description
Allowed Values
Arguments to pass to recon-all
Used to pass arguments to recon-all
alphanumeric
Use Manual QC to select "best" scan?
Select Yes to allow the pipeline
to automatically select best scan
based on the Manual QC
Select Yes or No
What are the scan types for T1 scans in your project?
Enter the labels for T1s on the
sessions in the project
alphanumeric
If you use them, what are the scan types for T2 scans in your project?
Enter the labels for the T2s on the
sessions in the project
alpahnumeric
If you use them, what are the scan types for FLAIR scans in your project?
Enter the labels for the FLAIR
sessions in the project
alphanumeric
Email Notification Settings
Used to automatically send notification
emails to users other than launcher
email addresses

Launch Inputs

Name
Description
Allowed Values
Determine Best Scan to Use
Used to manually select the scan to run the
pipeline on
select a scan
Select T2 Scan
Determine which T2 Scan from the project to use
(When available)
alphanumeric
Select FLAIR Scan
Determine which FLAIR Scan from the project to use
(When available)
alphanumeric
Advanced Parameters:
Recon-All Args
Used to pass arguments to recon-all
alphanumeric
Email Notification List
Used to automatically send notification
emails to users other than launcher
email addresses

Upload Corrections on a Previously run Freesurfer and Relaunch
  1. Navigate to the Freesurfer Report page.
  2. In Actions box, click Manage Files.
  3. On the File Manager dialog box, click Upload Files button.
  4. On the Upload File dialog box select:
    Level = resources
    Folder = Data
    Overwrite = checked

    UPloadManRoiDialog.jpg
  5. Click Browse, select file with corrections.
    • Must be a zip file.
    • Session name as root dir.
    • Subdirectories as needed -- tmp and/or mri.
      eg. editing control points only -- [sessionname]/tmp/control.dat
  6. Click Upload.
  7. Click Close.
  8. If needed, navigate back to the Freesurfer Report page.
  9. In Actions box, click Relaunch.
    Relaunch.jpg
  10. Click Submit Pipeline.
Note: The command being run on relaunch is: recon-all -make all

Outputs

The following will result from a successful completion of the pipeline:

  • The user who launched the pipeline will receive an email from the XNAT Team with the wording:
    "Freesurfer processing completed for..."
  • Files will be created in the Assessors/Freesurfer directory for the scan under the folders Data, Log, and Snapshots
  • On the Session Details page, a link to the Freesurfer Analysis Details page will display labelled as Freesurfer under the heading Assessments

Additional Information

FreeSurfer Software Suite

References

Fischl, B., 2012. FreeSurfer. Neuroimage 62, 774–781. doi:10.1016/j.neuroimage.2012.01.021

Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based analysis. I. Segmentation and
surface reconstruction. Neuroimage 9, 179-194.