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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

The Freesurfer_64bit_v5.1.xml pipeline is used for MR sessions with good quality T1 data such as MPRAGE.
The FS_forPETMR_64bit_v5.1.xml pipeline is used for PET sessions with good quality T1 data.

Project Inputs

Name
Description
Allowed Values
Launch pipeline automatically
when session is archived
Option to cause pipeline to run on a session as soon as it is
archived in the project
checked or unchecked
checked=yes
unchecked=no
mprs
The Scan type label for MPRAGE in the project
text
useall_t1s
Indicate if all T1s in the session should be used when running pipeline
0 or1
1=use all T1 scans
0=use first usable T1

Launch Inputs

Name
Description
Allowed Values
Check scans to include in build
Indicate which scan types should be included
checked or unchecked
checked=yes
unchecked=no
useall_t1s
Indicate if all T1s in the session should be used when running pipeline
checked or unchecked
checked=yes
unchecked=no
Send additional confirmation emails to
Allow emails of successful pipeline completion to be sent to
people other than the user running the pipeline
email addresses
separate by comma

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 under the heading Assessments.

Additional Information

FreeSurfer Patch
NRG Freesurfer Page

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.