{"id":20566172,"url":"https://github.com/aces/simulation_toolkit_singularity","last_synced_at":"2026-04-17T22:32:03.327Z","repository":{"id":139175343,"uuid":"372590029","full_name":"aces/simulation_toolkit_singularity","owner":"aces","description":null,"archived":false,"fork":false,"pushed_at":"2021-06-14T12:07:14.000Z","size":19,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-09-08T23:28:52.556Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aces.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-05-31T17:59:43.000Z","updated_at":"2021-07-12T19:04:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"fdee513e-49b5-4af3-bdec-5b46b9b3cf6e","html_url":"https://github.com/aces/simulation_toolkit_singularity","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/aces/simulation_toolkit_singularity","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fsimulation_toolkit_singularity","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fsimulation_toolkit_singularity/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fsimulation_toolkit_singularity/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fsimulation_toolkit_singularity/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aces","download_url":"https://codeload.github.com/aces/simulation_toolkit_singularity/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fsimulation_toolkit_singularity/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31948420,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-17T17:29:20.459Z","status":"ssl_error","status_checked_at":"2026-04-17T17:28:47.801Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-16T04:40:18.572Z","updated_at":"2026-04-17T22:32:03.289Z","avatar_url":"https://github.com/aces.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Simulation Toolkit for Coticometry Pipeline\n\nTools in this repository can be used to simulate artificial lesions in the brain in order to estimate the sensitivity and specificity of lesion\ndetection, using different automated corticometry pipelines.\n\nTo set up software you need the following:\n\n1. Install the software packages needed to run the deformation-2.pl script. Please follow steps in: https://github.com/aces/simulation_toolkit_singularity/blob/main/Singularity\n\n2. Obtain data from \nhttps://ida.loni.usc.edu/collaboration/access/appLicense.jsp;jsessionid=B0278AF5FD413E9AC14512DF841FFCA4/ \n\n3. Run deformation pipeline\"\n\nUsage\nUsage: deformation.pl -input \u003c.mnc\u003e -output \u003coutputdir\u003e [options] \n\nMandatory options:\n    \n    -deformation_ratio    provide the ratio of deformation, values must be between 0.1 [shrinkage] to 1.50 [expansion] [e.g. 0.1,1.2,0.6,…]\n    \n    -mask                 Specify a tolerance map file (.mnc) indicating voxels that have a different amount of error allowed e.g., CSF, background [e.g. your-mask.mnc]\n    \n    -coordinate           Specify a hyperslab starting at \u003cx\u003e \u003cy\u003e \u003cz\u003e and extending in respective directions by \u003csizex\u003e \u003csizey\u003e \u003csizez\u003e [e.g. 70 100 80 5 5 5]\n    \n    -tolerance_space      Define the buffer area around the deformation region [default = 4]\n    \n    \nOther options:\n    \n    -blur_determinant     Blurring kernel size for blurring deformation determinant blurring kernel 0-1\n    \n    -error                Specify the amount of error that is allowed between the specified determinant and the final determinant (per voxel) [default =0.00001]\n    \n    -iteration            Specify the maximum number of iterations to update the deformations field (-1 means until convergence) [default 1000]\n    \n\nExample:\n    \n  ./deformation.pl -input ICBM_00100_t1_final.mnc -output Debugging_Folder -deformation_ratio 0.6 -coordinate 70 100 70 10 10 10 -tolerance_space 4 -blur_determinant 0.25  -error 0.00001  -iteration 100 \n\n\nThe locally-deformed output file name includes input parameters to simplify creating GLM matrices for statistical analysis. \n    \nICBM_00100_t1_final_deformed_by_0.4atROIx70-y100-z70dimx10.dimy10.dimz10.mnc. \n\n\nThere following intermediate files are generated to help you do quality control and can be deleted:\n    \n/Debugging_Folder/TMP/block.mnc\n   \n/Debugging_Folder/TMP/blurred0.25determinant_r_0.4x70-y100-z70dimx10.dimy10.dimz10.mnc\n    \n/Debugging_Folder/TMP/DDDDdilated.mnc   \u003c\u003cnumber of D's corresponds to the number of times the tolerance space (defined to be 4 in the commandline) is dilated\n    \n/Debugging_Folder/TMP/DDDDring.mnc\n    \n/Debugging_Folder/TMP/determinant_r_0.4_grid.mnc\n    \n/Debugging_Folder/TMP/determinant_r_0.4x70-y100-z70dimx10.dimy10.dimz10.mnc\n    \n/Debugging_Folder/TMP/determinant_r_0.4.xfm\n    \n/Debugging_Folder/TMPmask.mnc\n    \nALTERNATIVELY: If you don't want to use this Perl wrapper, then follow the instructions for creating your own deformations:\nhttps://wiki.mouseimaging.ca/display/MICePub/Generating+deformation+fields\n\nSource code for deformation pipeline and dependencies (MINC):\nhttps://github.com/Mouse-Imaging-Centre/generate_deformation_fields\n\n    \n4. Example Data, Scripts and Statistical analysis used in our Frontier's Paper can be found here: https://github.com/aces/simulation_toolkit_statistics\n\n5. All these tools and data needed will be made available via CBRAIN. To learn more, please contact us at cbrain-support.mni@mcgill.ca. In the subject line, pleasee be sure to write SIMULATION TOOLKIT.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Fsimulation_toolkit_singularity","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faces%2Fsimulation_toolkit_singularity","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Fsimulation_toolkit_singularity/lists"}