External Email - Use Caution Hi Elizabeth,
the qatools / fsqc tools have evolved quite a bit since their inclusion in FS 7.1. Would it be possible for you to try their newest version, available from https://secure-web.cisco.com/1qVzbBOmbAq6CLsJURwFbYk1OnFTRlQmC3pOCUNhTJ-te1GfvL_15kWPyF0fH9XyN5BD7JT9r_ZvrY3V1uN7QAiFk9lTPE_avB3PIiO3Zevib0gCZlgU20LkuCEa7iP8KTq-Y6sbC8w_mTWW7ZeSFvFDDlCQY2jYf2k0d26bFb6dIDYblSdOMBHkc08XABRWShkn0fjvrxZY4uD94o-3_yB9Q53QYZknaab1tIKR7l1Z2UHZmc273nvQJ7bp71UPLVMA5DjhC1AHBvnjPqE2PQnP4mNi2bRwlitsdKXQvYjSyGY95OiPj_G864gDlc1-V04txwADGIOAV6KsdzJDg5A/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc? Thanks, Kersten On Thu, 2023-10-12 at 00:23 +0000, Elizabeth Haris wrote: CAUTION: This email originated from outside of DZNE. Do not click links or open attachments unless you recognize the sender and know the content is safe. ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim Anklicken von Links oder Öffnen von Anhängen External Email - Use Caution Hi there, I am running into a problem when using qatools.py to qa my recon-all. Some of my participants process ok, but with others I get the error below. Any advice on what to do to address this? Many thanks, Elizabeth ERROR: Computing white and gray matter SNR for orig.mgz ... Traceback (most recent call last): File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in <module> qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 883, in run_qatools _do_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 663, in _do_qatools wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, SNR_AMOUT_EROSION, ref_image="orig.mgz") File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/checkSNR.py", line 83, in checkSNR b_wm_data[x,y,z] = 1 IndexError: index 256 is out of bounds for axis 2 with size 256 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1iUrdCvvH-tTUh-ud1LBZ9GCsUXuG71YyUtho4dl56eyP6h-47L0ngQxRPQEdBtgBYn3Ed4DQr36WwZonCvrDHKAKSRa6JhtquC3pg9KQYRaUdP0VM-8dW1I7Jqn1mFtjl-zSwR8yaDe0CoumcD2ZQVSrMENnQxIOAP_4xJsDaegoaj6EuHpXgTuPRfWvbFuWKZUATxxSruNvUETGLYgtHoAnf92ZY7cftvQI4kNGDRbB3_hO9ZhDjHCmom0rE2rRFVFxqDsm7QUI7QiMGx_m3Ocuc3bbDIutQnhF6gmdEV7pqODqGbbGXUKLxE8pA5DGIdgDhPjlSm0eR5Rdbs6QXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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