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Hi FS experts,
I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here: https://secure-web.cisco.com/1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPj... and placed the scripts in their designated directories. However, I received the same error as before. The output indicates that the core.py script is located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, as opposed to the directory I was instructed to put the core.py script in ('$FREESURFER/python/packages/gems/subregions/').
Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another course of action that I can do that may solve this issue?
Here is the exact error, if that is at all helpful: Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp'
Thank you in advance for your help!
Best Wishes, Katie -- Katie Jobson, M.S. | Personal Websitehttps://secure-web.cisco.com/1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athVw1rlGDJ6sTy7yVFFWJBkSfhVQs-ERcG_L3oXVWMADGT5-tV7LBBMD7EwnhGiZ7MRrBYfbM-Ixh6qioHPgeLskxYOWAtLdvG0uVkpYDbsL4C8Z8zWouSr6bSlWKv0B371bqES3dXSF47F_fPyYE42XsPkmkPY07cWlBAroKO4MyOxUb06ONSnmYxdXAU5ab0f9c9ju6MfbHg4IieU1ECtqao1fw5H-Idta06FlDqn0v-TZczEyQMz_yMfoy_oA9QOWJyEEHIR8J_vHzH15DhUBUgx2gtv0kuE0ZGjebQjQ/https%3A%2F%2Fkjobson-neuro.github.io%2F Ph.D. Student | Cognitive Neuroscience Labhttps://secure-web.cisco.com/13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjVw3vQ9lQCBGRAJDIhWHwLmtZ2hMLLSzCRhoKz3qo97Q472xVV0I-dmZKJahUOBAnwchKxLdDQOJkxntBsA4NbWyxrDP80dMWcPZDA9hqpjtMzmYRZkXbbJ2F_QL3hqIhlTcczsRrBZermR0RF0-ZR5oKet9KHvjxlgAd8PJgZ573QiqJ96Hgi0xdHBzG9Kh6cYkwtkoU3L-6UGBdsfGFBSQJ1BaGfIWPLl0-CgB5KwOWekN7AXJGHOF6gyZimhtMxIS-7421h7RZu67mW74Jb6sS5UnRLAp7G-p66Jyrlw/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F Department of Psychology and Neuroscience | Temple University