{"id":24308054,"url":"https://github.com/atrotier/seq_bruker_a_mp2rage_cs_public","last_synced_at":"2025-09-26T14:30:43.148Z","repository":{"id":127724499,"uuid":"274076839","full_name":"aTrotier/SEQ_BRUKER_A_MP2RAGE_CS_PUBLIC","owner":"aTrotier","description":"Compiled sequence and reconstruction of the MP2RAGE + CS sequence for Bruker scanner","archived":false,"fork":false,"pushed_at":"2024-03-06T10:00:02.000Z","size":620,"stargazers_count":3,"open_issues_count":2,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-03-06T11:04:31.385Z","etag":null,"topics":["bruker","compressed-sensing","mp2rage","mri","t1","t1map"],"latest_commit_sha":null,"homepage":"","language":"C++","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/aTrotier.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}},"created_at":"2020-06-22T08:04:20.000Z","updated_at":"2023-09-04T03:03:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"ecf95652-d44b-4bbe-b2ed-f2a58ca1ffa1","html_url":"https://github.com/aTrotier/SEQ_BRUKER_A_MP2RAGE_CS_PUBLIC","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aTrotier%2FSEQ_BRUKER_A_MP2RAGE_CS_PUBLIC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aTrotier%2FSEQ_BRUKER_A_MP2RAGE_CS_PUBLIC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aTrotier%2FSEQ_BRUKER_A_MP2RAGE_CS_PUBLIC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aTrotier%2FSEQ_BRUKER_A_MP2RAGE_CS_PUBLIC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aTrotier","download_url":"https://codeload.github.com/aTrotier/SEQ_BRUKER_A_MP2RAGE_CS_PUBLIC/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":234314435,"owners_count":18812696,"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":["bruker","compressed-sensing","mp2rage","mri","t1","t1map"],"created_at":"2025-01-17T04:47:18.364Z","updated_at":"2025-09-26T14:30:42.492Z","avatar_url":"https://github.com/aTrotier.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bruker Sequence : MP2RAGE + Compressed Sensing acceleration\n\nThis repository regroups the compiled sequence and matlab reconstruction of the MP2RAGE+CS sequence. This repository is still in **beta** don't hesitate to open a issue and share your comments.\n\n\n\nSequence principle is described in this MRM publication :  [![DOI](https://zenodo.org/badge/DOI/10.1002/mrm.27438.svg)](https://doi.org/10.1002/mrm.27438)\n\n**Source code is available as a private [submodule](https://github.com/aTrotier/SEQ_BRUKER_A_MP2RAGE_CS_PUBLIC)** if you want the source code, send a request to : \u003caurelien.trotier@rmsb.u-bordeaux.fr\u003e\n\n\n\n## Plan\n\n- [Bruker Sequence : MP2RAGE + Compressed Sensing acceleration](#bruker-sequence--mp2rage--compressed-sensing-acceleration)\n  - [Plan](#plan)\n  - [Folder structure](#folder-structure)\n  - [Sequence installation](#sequence-installation)\n  - [Acquisition](#acquisition)\n\n## Folder structure\n\n* **SEQ** : Binary the sequence on Bruker scanner (PV6.0.1).\n* **RECO_a_MP2RAGE_CS** : Reconstruction available in matlab and Julia\n  * **RECO_JULIA_A_MP2RAGE_CS** : Offline and online reconstruction through macro\n  * **RECO_MATLAB_A_MP2RAGE_CS**\n    * **script_T1MAP_MP2RAGE.m** is the main script to reconstruct the T1 maps\n    * **simu folder** : regroup script to find optimal parameters for acquisition and reconstruction\n      * **opti_reco** folder : script to find the optimal parameters for reconstruction\n      * **opti_acq** folder : various script to analyze the acquisition parameters effect\n\n\n## Sequence installation\n\nSequence has been developped for Paravision **PV6.0.1**. Minor modification are required for PV6.0 compatibility (feel free to contact us)\n\n**Installation step :**\n\n* Copy the binary sequence under the folder\n  `/opt/PV6.0.1/share/`\n\n* To install : `File -\u003e Import -\u003e Binary Method ` and select the sequence in the share folder.\n\n\nSequence is now install and available under the **Palette** tab/Explorer tab/Scan Programs \u0026 Protocols :\n\n```\nObject : AnyObject\nRegion : AnyRegion\nApplication : UserMethods\n```\n\nTo use it drag and drop to an exam card.\n\n## Acquisition\n\nWe will only described the MP2RAGE specific parameters. The other ones are standard (Sequence is based on the Bruker FLASH sequence). The parameter name in the bruker card is in **bold**. In brackets are the corresponding names in the publication.\n\n* ROUTINE tab\n\n  * **Repetition Time** (TR) : is the time between 2 excitations within GRE blocks\n\n  * **Recovery Time** (MP2RAGETR) : is the time between 2 inversions pulses\n\n  * **Flip Angle TI1** and **Flip Angle TI2** : correspond of the excitation flip angle of the first and second GRE Blocks\n\n  * **Train Echo**  : is the number of echos per GRE readout\n\n  * **Effective TI** (TI1/TI2) : correspond to the time between inversion and the middle of each GRE blocks.\n\n  * **Acceleration Type** :\n\n    * **Fully** : no acceleration, all k-space is encoded (if the **Echo Train is equal to the ky matrix size. The image will be directly reconstructed under Bruker)\n    * **Grappa** (WIP -\u003e supposed to work, just check the mask to be sure)\n    * **Compressed sensing** :\n      * **Mask_With_File** : *deprecated* (if you need to use your own mask contact us)\n      * **Mask_With_algorithm** : if you change any parameters don't forget to click on **CalcMask**\n\n    \u003e Both Grappa and Compressed use **Acceleration CS Y/Z** so choose your acceleration and click on **CalcMask**. It indicates the total acceleration **Acceleration Totale** (French :D).\n    \u003e\n    \u003e **Size of center mask** indicates the size of the squared fully sampled central part of the k-space (Used later for coil sensitivity calibration)\n    \u003e\n    \u003e **GenpointMask** : the mask algorithm generates a number of ky/kz lines which can not be a multiple of the **Train Echo**. Thus, we do not acquire some lines at the bottom of the k-space, in order to remain a multiple. The number of non-acquired lines is called the **GenpointMask**\n\n    **AGAIN : Don't forget to click on CalcMask**\n\n* Contrast tab / Sel IR : You can change the inversion pulse parameters\n\n  * Usually we use a sech of 10 ms with a slab Thickness of 200%\n\n* Sequence tab / Main : You can change the excitation pulse parameters\n\n  * Usually we use sinc10H of 1ms\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fatrotier%2Fseq_bruker_a_mp2rage_cs_public","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fatrotier%2Fseq_bruker_a_mp2rage_cs_public","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fatrotier%2Fseq_bruker_a_mp2rage_cs_public/lists"}