PET_SURFACE

[Remi Silva]

Hi,

I am trying to run the pet surface for PIB tracer. I have been having issues with the psf file but it seems to have worked when i changed the tracer column from 11CPIB to Tracer.PIB as this is what the error message was flagging.

RuntimeError: Subject sub-ADNI041S1411 with session ses-M000 and tracer Tracer.PIB that you want to proceed was not found in the TSV file containing PSF specifications

However, I am now having problems with the CAPS directory. Here is the error message:

FileNotFoundError: [Errno 2] No such file or directory: '/mnt/scratch/users/rs2472/OUTPUT_SURFACE/CAPS_SBM/subjects/sub-ADNI041S1420/ses-M000/t1/freesurfer_cross_sectional/sub-ADNI041S1420_ses-M000/surf/lh.white_exp-007'

and here is a screenshot of my CAPS directory with the filepath at the top:

[Nicolas Gensollen]

Hi,

This error has been reported before (see https://github.com/aramis-lab/clinica/issues/890 and https://github.com/aramis-lab/clinica/issues/1103) but it doesn't seem like a solution was found and implemented.

As it seems to be popping up every once in a while, I suspect there is something wrong at this stage of the PETSurface pipeline.

I'm going to take a closer look in the next few days and will let you know what I could find.

On the positive side, I'm glad you were able to solve your previous issue with the PSF specifications.

Best,

Nicolas