Question about alias/symlink files in FreeSurfer "surf" directory after t1-freesurfer

[Muhammad Orhan]

Hi Clinica Team,

During t1-freesurfer processing, I noticed that for some subjects a few files inside the surf folder appear as aliases (symlinks) rather than original files, as shown in the attached screenshot. This does not happen for all subjects.

Is this expected behaviour in FreeSurfer, or does it indicate a problem with the reconstruction?
More importantly, could these symlink files affect the PET-Surface pipeline later on, or is Clinica designed to work with them without issues?

Setup: MAC-M3, Clinica 0.94 / 10.1, FreeSurfer: (freesurfer-macOS-darwin_x86_64-7.4.1)

Thanks in advance for your help!

Best regards,

Muhammad

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[Alice Joubert]

Hello Muhammad,

Indeed this could indicate a process completion issue and I don't think pet-surface is able to handle symlinks. I will try to test this case next week if I have time. Does this represent a lot of your subjects? 

Best,

Alice

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[Muhammad Orhan]

Hello! A. Joubert,
Thanks.. that would be great if you test this.
I faced this issue with around 400 subjects from a cohort of 1500.

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[Alice Joubert]

Hello Muhammad,

Sorry for the delay. I tried to reproduce the bug with subject `003_S_1122`, first session. I could not even create a bids for the image as it does not pass our converter QC check. How did you obtain your nifti for it ?

Best,

Alice