Hi, I am wondering if the freesurfer longitudinal stream is implemented in QuNex. If not, I’d appreciate any advice on how to integrate the outputs of recon-all -long into the QuNex data hierarchy and workflow. Thanks in advance for the help!
I am using QuNex v0.90.6
Hey Charlie! The FreeSurfer longitudinal stream is not currently supported although we are hoping to integrate it in the future. I can provide advice from my own experience with the longitudinal pipelines but please bear in mind that this is not the official QuNex implementation.
Personally I have had success placing the subject templates in the hierarchy like so:
<study>/sessions/templates/<subject_id>/TemplateA/
And making symbolic links to the individual timepoints (ie. session Freesurfer output folders) within that. You should then be able to run the template creation step of the longitudinal FS stream. In this example TemplateA is just a name you can give to distinguish this template from any others you might want to create for that subject.
To run the longitudinal FS run itself, I symlinked the template folder and the Freesurfer folders for the other time-points into:
<study>/sessions/<session_id>/hcp/<session_id>/T1w
e.g.
ln -s <study>/sessions/<sub1_session2>/hcp/<sub1_session2>/T1w/<sub1_session2> <study>/sessions/<sub1_session1>/hcp/<sub1_session1>/T1w/
and
ln -s <study>/sessions/templates/<subject_id>/TemplateA <study>/sessions/<sub1_session1>/hcp/<sub1_session1>/T1w/
You can then rerun FreeSurfer with the -long option and it will create outputs in:
<study>/sessions/<sub1_session1>/hcp/<sub1_session1>/T1w/<sub1_session1>.long.TemplateA
I hope that helps!
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Hi Lisa, good to hear from you, hope you’re doing well! Thanks a ton for the answer, that is very helpful.
Would the simplest way to process the FS -long outputs through hcp_post_freesurfer etc. in QuNex be to symlink the FS -long output to the expected naming and location for hcp_post_freesurfer inputs (after renaming the original hcp_freesurfer outputs)? Thanks!
Yes, that should work as a temporary solution!
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