Summary of what happened:
Hello there, I tried posting on the FSL list but I’m not able to for some reason.
I have a bunch of topup/eddy preprocessed files with eddy_quad run on them successfully. I’ve also successfully run eddy_squad on those outputs to get group descriptive stats. Now I want to “update” the single subject quad runs so that the little stars appear within the violin plots, effectively pointing out where within the group a particular subject is found (see, e.g. Bastiani et al 2019 figs 2 and beyond).
At this final step eddy_squad seems to choke in the middle of processing the first subject. It leaves correct-looking “qc_tables_tmp.pdf” and “qc_tmp.pdf” files, but then errors out with:
eddy_squad --update squad/group_db.json squad/quad_list.txt
/wynton/protected/home/rad-wynton-only/storrisi/fsl/bin/eddy_squad:4: DeprecationWarning: pkg_resources is deprecated as an API. See [https://setuptools.pypa.io/en/latest/pkg_resources.html](https://urldefense.com/v3/__https://setuptools.pypa.io/en/latest/pkg_resources.html__;!!LQC6Cpwp!oedflVYqokwmxv8B5XwvH4awhj3t7fwDQhbiOifFaAWhOrfW0NUez8lbKEYfH_7hOuAVLblrBUjYxwFAeWV7yzlo7kk$)
import pkg_resources
Reading group database...
Group database imported.
Updating single subject reports...
Traceback (most recent call last):
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/bin/eddy_squad", line 39, in <module>
main(args.list, args.grouping, args.group_db, args.update, args.output_dir)
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/lib/python3.12/site-packages/eddy_qc/SQUAD/squad.py", line 146, in main
squad_update.main(db, sList, group, group_db)
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/lib/python3.12/site-packages/eddy_qc/SQUAD/squad_update.py", line 166, in main
file1 = PdfFileReader(line + '/qc_tables_tmp.pdf', 'rb')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/lib/python3.12/site-packages/PyPDF2/_reader.py", line 1974, in __init__
deprecation_with_replacement("PdfFileReader", "PdfReader", "3.0.0")
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/lib/python3.12/site-packages/PyPDF2/_utils.py", line 369, in deprecation_with_replacement
deprecation(DEPR_MSG_HAPPENED.format(old_name, removed_in, new_name))
File "/wynton/protected/home/rad-wynton-only/storrisi/fsl/lib/python3.12/site-packages/PyPDF2/_utils.py", line 351, in deprecation
raise DeprecationError(msg)
PyPDF2.errors.DeprecationError: PdfFileReader is deprecated and was removed in PyPDF2 3.0.0. Use PdfReader instead.
Command used (and if a helper script was used, a link to the helper script or the command generated):
eddy_squad --update squad/group_db.json squad/quad_list.txt
Version:
FSL ver 6.0.7.15
Environment (Docker, Singularity / Apptainer, custom installation):
i’m within a Conda environment on an HPC cluster. is PdfReader something i could add to my environment, should i do the teeny incremental FSL update to 6.0.7.16, or has this not been updated in eddy_squad itself?
thanks!
-Sam