{"id":18142424,"url":"https://github.com/benoitberanger/mp2rage","last_synced_at":"2025-04-22T20:33:19.371Z","repository":{"id":43339771,"uuid":"172770355","full_name":"benoitberanger/mp2rage","owner":"benoitberanger","description":"SPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts","archived":false,"fork":false,"pushed_at":"2024-02-27T14:56:54.000Z","size":4790,"stargazers_count":10,"open_issues_count":2,"forks_count":6,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-29T18:36:33.359Z","etag":null,"topics":["mp2rage","mri","spm","spm12"],"latest_commit_sha":null,"homepage":null,"language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/benoitberanger.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2019-02-26T18:52:14.000Z","updated_at":"2024-12-26T01:59:50.000Z","dependencies_parsed_at":"2024-02-27T16:05:37.357Z","dependency_job_id":null,"html_url":"https://github.com/benoitberanger/mp2rage","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2Fmp2rage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2Fmp2rage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2Fmp2rage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2Fmp2rage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/benoitberanger","download_url":"https://codeload.github.com/benoitberanger/mp2rage/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250318993,"owners_count":21411029,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["mp2rage","mri","spm","spm12"],"created_at":"2024-11-01T18:21:57.141Z","updated_at":"2025-04-22T20:33:19.320Z","avatar_url":"https://github.com/benoitberanger.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mp2rage\nSPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts  \nBased on :\n* O'Brien KR, Kober T, Hagmann P, Maeder P, Marques J, Lazeyras F, et al. (2014) Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. PLoS ONE 9(6): e99676. https://doi.org/10.1371/journal.pone.0099676\n* O'Brien K, Krueger G, Lazeyras F, Gruetter R, Roche A, A simple method to denoise MP2RAGE; 2013; Salt Lake City, Utah.pp. 269. http://archive.ismrm.org/2013/0269.html\n* Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., Van de Moortele, P.-F., \u0026 Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. https://doi.org/10.1016/j.neuroimage.2009.10.002\n\n## Requirements\nSPM12 : https://www.fil.ion.ucl.ac.uk/spm/software/spm12/\n\n\n## Installation\nClone the repo : `git clone https://github.com/benoitberanger/mp2rage`,\nor use direct download link [\u003e\u003e here \u003c\u003c](https://github.com/benoitberanger/mp2rage/archive/master.zip),\nthen place freshly downloaded/cloned directory in `spm12/toolbox/`, such as `spm12/toolbox/mp2rage`.\nYou can also use a symlink, such as `ln -s path/to/mp2rage path/to/spm12/toolbox/mp2rage`\n\nThat's all.\n\nIf you already started SPM in your MATLAB session, don't forget to refresh SPM paths with `spm_jobman('initcfg');`.\n\n\n## How it works\nThis repo is an extension of _spm12_, you can use the Batch Editor (`spm_jobman`) and open the tab SPM \u003e Tools \u003e MP2RAGE \u003e choose-your-job\n\n### Remove background\nThe objective is to remove the \"salt and pepper\" background noise from the UNI image.  \n\n#### Method 1 (newer)\nUse a INV2 as pseudo mask. No user tuning required.  \nBased on : https://github.com/srikash/3dMPRAGEise.git\n\n#### Method 2 (historical)\nUse a INV1 + INV2 + regularisation factor. The regularisation factor has to be tuned by the user.  \nBased on :\n* O'Brien KR, Kober T, Hagmann P, Maeder P, Marques J, Lazeyras F, et al. (2014) Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. PLoS ONE 9(6): e99676. https://doi.org/10.1371/journal.pone.0099676\n* O'Brien K, Krueger G, Lazeyras F, Gruetter R, Roche A, A simple method to denoise MP2RAGE; 2013; Salt Lake City, Utah.pp. 269. http://archive.ismrm.org/2013/0269.html\n\n#### Interactive\nTo determine which regularization factor to use, you can use the job SPM \u003e Tools \u003e MP2RAGE \u003e Interactive remove background  \nThis will display the original UNI image and the denoised version with a popup where you can enter the regularization level and check the result immediately :  \n![irmbg](https://github.com/benoitberanger/mp2rage/blob/master/example/interactive_rmbg.gif)\n\n#### Normal\nWhen you are settled with your regularization level, use \"normal\" job SPM \u003e Tools \u003e MP2RAGE \u003e Remove background :  \n![rmbg](https://github.com/benoitberanger/mp2rage/blob/master/example/rmbg_gui.png)\n\n### Estimate T1\nThis job will estimate T1map and R1map using sequence parameters and the UNI image.  \nBased on :\n* Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., Van de Moortele, P.-F., \u0026 Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. https://doi.org/10.1016/j.neuroimage.2009.10.002\n\n![estimateT1](https://github.com/benoitberanger/mp2rage/blob/master/example/estimateT1.png)\n\n#### Comments on the parameters\n| Parameter name                 | Description                           | dcm2niix json sidecar field   | on Siemens scanners                                |\n|--------------------------------|---------------------------------------|-------------------------------|----------------------------------------------------|\n| UNI image                      | input T1 weighted                     |                x              | this image has the suffix `\\_UNI_image`            |\n| Magnetic field strength B0 (T) | in Tesla (T)                          | MagneticFieldStrength         |                           x                        |\n| MR2RAGE TR (s)                 | Repetition time (TR) of the MP2RAGE   | RepetitionTime                | TR                                                 |\n| EchoSpacing (s)                | in seconds (s), TR of the GRE readout | **does not exist**            | tab Sequence \u003e Part 1 \u003e Echos pacing               |\n| Inversin Times (s)             | in seconds (s), such as `[TI1 TI2]`   | InversionTime                 | TI                                                 |\n| Flip Angles (°)                | in degree (°), such as `[FA1 FA2]`    | FlipAngle                     | Flip angle                                         |\n| Number of slices per slab      | Number of slices per slab             | **does not exist**            | Slices per slab                                    |\n| PartialFourierInSlice          | The value range is 0 to 1             | PartialFourier                | **SlicePartialFourier**, not PhasePartialFourier \u003cbr\u003e expressed as a fraction such as 8/8, 7/8, ... | \n| Fat saturation pulse           |                    x                  | **does not exist**            | tab Contrast \u003e Fat Sat \u003cbr\u003e the option can be \"nonce, \"water excitation normal\", \"water excitation fast\" |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Fmp2rage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenoitberanger%2Fmp2rage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Fmp2rage/lists"}