External Email - Use Caution
Hi, I saw this thread and was wondering about the details of this patch. Does this patch affect the standard recon-all call or is this meant for a special flag. Also I was also wondering what issue did it solve? Thank you.
On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish Avnish.Kumar@mgh.harvard.edu wrote:
Hi Katie,
The core.py file has been updated now. Please try downloading it again and applying the same fix https://secure-web.cisco.com/1jL26L7yFavOUgcWfxYm-k3h15hb0c5gOBHa9Fed4BCYLubpwr-niyJ-R1e6v30g6M7KnS_6WZxqflmAWLgjRPfEPSuoq0dklfegUn03H-r36juVobk3F3SYqLW5gq23xrLQiPF5G2vENSKbNdvxNLPIgVwOC0_84R3mVkvdBCElZhtZ5UDlXd0WzMLSjf7gJDbB651AHUCT9wh-91j-A0iUNu79mTXPZtmayJ77YNgMlH9qiSwRzhRT0H2iC6FCqMgCLC7PinAV99aNZo4EAzLIQZNZ4fOtEjm51OZZ4T_077e6kprzhNwFhcMaW-CIBATU8VSigXdH9B-i_aPvXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Fsegment_subregions%2F as before.
Best, Avnish
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson < katie.jobson@temple.edu> *Sent:* Monday, February 6, 2023 3:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation
External Email - Use CautionHi FS experts,
Apologies for my late follow up.
In reference to the previous conversation, I added the core.py file to the correct subdirectory to complete the thalamic nuclei segmentation. I received an error still, albeit a different error:
Traceback (most recent call last):
File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, in <module>
from freesurfer import subregionsFile "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py", line 1, in <module>
from freesurfer.subregions.process import structure_namesFile "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 8, in <module>
from freesurfer.subregions.thalamus import ThalamicNucleiFile "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py", line 9, in <module>
from freesurfer.subregions.core import MeshModelFile "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 9, in <module>
from gems.subregions import utilsImportError: cannot import name 'utils' from 'gems.subregions' (unknown location)
I am assuming this is because the core.py script was previously housed in the '/gems/subregions' subdirectory, and is attempting to import 'utils' from there. Is there any way to edit this file (core.py) to call on this 'utils' function?
Please let me know if I can clarify my question in any way and thank you in advance for your help!
Best Wishes, Katie -- Katie Jobson, M.S. | Personal Website https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F Ph.D. Student | Cognitive Neuroscience Lab https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F Department of Psychology and Neuroscience | Temple University
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kumar, Avnish < Avnish.Kumar@mgh.harvard.edu> *Sent:* Thursday, December 8, 2022 10:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation
Hi Katie,
Thank you for pointing this out! Yes, please make changes to the core.py script in your '$FREESURFER/python/packages/freesurfer/subregions/' folder. I will update the patch instructions to reflect this as well.
Best, Avnish
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson < katie.jobson@temple.edu> *Sent:* Wednesday, December 7, 2022 3:35 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] 7.3.2-patch issues - thalamic segmentation
External Email - Use CautionHi 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: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1mCHS2GkeGhBpJl5i4kLOmiu-VYhuxPl9ZPOae6mcel-DbG... https://secure-web.cisco.com/1t1MSwicSbVaKTZz26QQcqNH4nacgccE3ISyro01uNnj95812z_YeG8e-DFrygCnFv6ktzMUExhmiUbDqFCf0KpNXHr5RRUcxC1AVcCaSsWWiaxtTasb5Nv7Ri_-7l4aFJc-3z8v4jMcuMuarQHkVMdfQFpDlwx_JPNCkzIF5bYbOAbLpgF5bFi1S7RGHvbfQJzCvT-GHwedW82ZkC0XRXlRJuOk5tvcxrjxhnlP_J0o1XiFpmUB27GQrmlDo4RruZFSRCORXtarTTjw4Ev2G9p7K_-aX2-nkBsHZuSRRYBIEgbqijea_xNPhBMogTCeJ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPjNtpIrfTSk2Oor44j2FBUk_pFk20EpHFiM3R1FVkDnc65JJPCI2jaG74UkvfjSzqwjWygwvquVzF3AUampB5BRXbiKSY7Eq72Qbr3mY5H5t3RtHvfghMkNSXw1ggCZ3hzozbWLX2XVfU6Y5rB9JzogJtWSki-SikTk1LjM-Zp5AqdAc4RDMLOPK5MST93Dqz207lgJp4Isj6YZIOqM1Fms1_LkZdkfuWRZVT-8jSSycyBTF13XHfqQC3TqOL541UgCoyh-f4b9wH1mNOwjdTyfJIP8epMLDFkafQf_-Ow%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Fpub%25252Fdist%25252Ffreesurfer%25252F7.3.2-patch%25252Freadme.txt%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DHp5cWxnS%252FQSuB9KV%252FgLBR53k3jfPkdqNqn9O5E2haNg%253D%26reserved%3D0 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 Website https://secure-web.cisco.com/1qpE5cLLOL2CHnskATS2LqMgtMkQTCjvU4-ECsmcad-ykS4zLMlXgZ588AmpaseiaPCkUvGQ1X4WspXesw0YnXcGOjyj0EijWmOKOXyotE1hV03fl4mXxOVIG2WKrYCf5A1FLFBA_YxNW-rvLNNcfqq56KBAFWvkOZqPUNORHUvLmwM1hJtOq6S-dINpVeZ_kOr4p6JZWf2yK1VRmbot0IkDKqCD3ylXwQZqnGd3xFGJBRyvqcwOgNqdslOi9c3kBXuuMhEYgOogGPHoha0q9Cg-Lq1dVlL0tfo188LWTwffgpnMDCUr0wcNHbRQsI4KU/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athVw1rlGDJ6sTy7yVFFWJBkSfhVQs-ERcG_L3oXVWMADGT5-tV7LBBMD7EwnhGiZ7MRrBYfbM-Ixh6qioHPgeLskxYOWAtLdvG0uVkpYDbsL4C8Z8zWouSr6bSlWKv0B371bqES3dXSF47F_fPyYE42XsPkmkPY07cWlBAroKO4MyOxUb06ONSnmYxdXAU5ab0f9c9ju6MfbHg4IieU1ECtqao1fw5H-Idta06FlDqn0v-TZczEyQMz_yMfoy_oA9QOWJyEEHIR8J_vHzH15DhUBUgx2gtv0kuE0ZGjebQjQ%252Fhttps%25253A%25252F%25252Fkjobson-neuro.github.io%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DjEfWDE9dwjIKlP1UEcWXaH0JOt7RZpZ3jDLG04rOwkQ%253D%26reserved%3D0 Ph.D. Student | Cognitive Neuroscience Lab https://secure-web.cisco.com/12TSjlFST5ClRU5NTmGCTo4cbHr9K_otNLC_UTGVRjTnEqOipmFiPU6ncsH260zbu8XMGDxbprbJihlBWCHuNLKEPzTwtMbjvLVM1N1J_GfvuOQyP82VGJKvv_mhN_my1bKZDe6OUxVOdT8ADJ6ewdd4NnK2HTiOb6QIYpUsqaOG1A7JWhhJzaaButMw8NGfeDvXf4ZR74JzKeAcjeOF8en6J11tcClnh_614PFl6j92ksk2WruYc_yTEFFVqWgCLfNCS3huT3d--QYSYRAzEGkulM6lXmAmuMfVf2oSDRaWseMO20bdLl-MyKDXJ1Z8s/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjVw3vQ9lQCBGRAJDIhWHwLmtZ2hMLLSzCRhoKz3qo97Q472xVV0I-dmZKJahUOBAnwchKxLdDQOJkxntBsA4NbWyxrDP80dMWcPZDA9hqpjtMzmYRZkXbbJ2F_QL3hqIhlTcczsRrBZermR0RF0-ZR5oKet9KHvjxlgAd8PJgZ573QiqJ96Hgi0xdHBzG9Kh6cYkwtkoU3L-6UGBdsfGFBSQJ1BaGfIWPLl0-CgB5KwOWekN7AXJGHOF6gyZimhtMxIS-7421h7RZu67mW74Jb6sS5UnRLAp7G-p66Jyrlw%252Fhttps%25253A%25252F%25252Fsites.temple.edu%25252Fcnltu%25252F%26data%3D05%257C01%257Ckatie.jobson%2540temple.edu%257C3795cd2b1f9a46dc040308dad92faa19%257C716e81efb52244738e3110bd02ccf6e5%257C0%257C0%257C638061096005588355%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsET5lqz9mj2jA3PqXIxjw2nZEIak3%252B7pJn4PEMboBQc%253D%26reserved%3D0 Department of Psychology and Neuroscience | Temple University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SjFuqM4yaBEvrnsDzwGCZgl1spW_bbpTmf1vxsEJsGExwi... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Mrl34OlVJbBPX3OPnuFmmU0QC4-lWSesE7KOyCRdPV_aja... < https://secure-web.cisco.com/1Mrl34OlVJbBPX3OPnuFmmU0QC4-lWSesE7KOyCRdPV_aja... .