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6 | 6 |
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8 | 8 |
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9 |
| -Rawdata for tests are available here : https://zenodo.org/records/14046657 |
| 9 | + |
| 10 | + |
| 11 | +Rawdata for tests are available here : https://zenodo.org/records/14046657 |
| 12 | + |
| 13 | + |
| 14 | + |
| 15 | + |
| 16 | +--- |
| 17 | + |
| 18 | +| **Documentation** | **Paper** | |
| 19 | +|:------------------------- |:--------------------------- | |
| 20 | +| [![][docs-img]][docs-url] | [![][paper-img]][paper-url] | |
| 21 | + |
| 22 | + |
| 23 | + |
| 24 | +SEQ_BRUKER_a_MP2RAGE_CS_360.jl is a Julia package that implements a reconstruction for an accelerated MP2RAGE sequence for Bruker scanner (**PV360-3.5**). |
| 25 | +The reconstruction is performed using MRIReco.jl |
| 26 | + |
| 27 | +More information and examples are available in the article [![][paper-img]][paper-url] and in the [![][docs-img]][docs-url] |
| 28 | + |
| 29 | + |
| 30 | + |
| 31 | +## How to give credit |
| 32 | + |
| 33 | +If you use this package please acknowledge us by citing : https://doi.org/10.1002/mrm.27438 |
| 34 | + |
| 35 | +Additionally, if you use the sequence available in the MR sequence folder, please contact us to sign the sequence transfer agreement : aurelien.trotier@rmsb.u-bordeaux.fr |
| 36 | + |
| 37 | +## Bruker sequence and protocol |
| 38 | + |
| 39 | +The sequence, implemented for **Bruker Paravision PV-360.3.5**, and the corresponding protocol for fully-sampled is available in the folder `MR sequence/PV-360.3.5`. Source code is available in this private directory : https://github.com/aTrotier/a_MP2RAGE_CS_360 |
| 40 | + |
| 41 | +## Julia Installation |
| 42 | + |
| 43 | +To use the code, we recommend downloading Julia version 1.10 with `juliaup`. |
| 44 | + |
| 45 | +<details> |
| 46 | +<summary>Windows</summary> |
| 47 | + |
| 48 | +#### 1. Install juliaup |
| 49 | +``` |
| 50 | +winget install julia -s msstore |
| 51 | +``` |
| 52 | +#### 2. Add Julia 1.10.4 |
| 53 | +``` |
| 54 | +juliaup add 1.10.4 |
| 55 | +``` |
| 56 | +#### 3. Make 1.10.4 default |
| 57 | +``` |
| 58 | +juliaup default 1.10.4 |
| 59 | +``` |
| 60 | + |
| 61 | +<!---#### Alternative |
| 62 | +Alternatively you can download [this installer](https://julialang-s3.julialang.org/bin/winnt/x64/1.7/julia-1.9.3-win64.exe).---> |
| 63 | + |
| 64 | +</details> |
| 65 | + |
| 66 | + |
| 67 | +<details> |
| 68 | +<summary>Mac</summary> |
| 69 | + |
| 70 | +#### 1. Install juliaup |
| 71 | +``` |
| 72 | +curl -fsSL https://install.julialang.org | sh |
| 73 | +``` |
| 74 | +You may need to run `source ~/.bashrc` or `source ~/.bash_profile` or `source ~/.zshrc` if `juliaup` is not found after installation. |
| 75 | + |
| 76 | +Alternatively, if `brew` is available on the system you can install juliaup with |
| 77 | +``` |
| 78 | +brew install juliaup |
| 79 | +``` |
| 80 | +#### 2. Add Julia 1.10.4 |
| 81 | +``` |
| 82 | +juliaup add 1.10.4 |
| 83 | +``` |
| 84 | +#### 3. Make 1.10.4 default |
| 85 | +``` |
| 86 | +juliaup default 1.10.4 |
| 87 | +``` |
| 88 | + |
| 89 | +<!---#### Alternative |
| 90 | +Alternatively you can download [this installer](https://julialang-s3.julialang.org/bin/mac/x64/1.7/julia-1.9.3-mac64.dmg)---> |
| 91 | + |
| 92 | +</details> |
| 93 | + |
| 94 | +<details> |
| 95 | +<summary>Linux</summary> |
| 96 | + |
| 97 | +#### 1. Install juliaup |
| 98 | + |
| 99 | +``` |
| 100 | +curl -fsSL https://install.julialang.org | sh |
| 101 | +``` |
| 102 | +You may need to run `source ~/.bashrc` or `source ~/.bash_profile` or `source ~/.zshrc` if `juliaup` is not found after installation. |
| 103 | + |
| 104 | +Alternatively, use the AUR if you are on Arch Linux or `zypper` if you are on openSUSE Tumbleweed. |
| 105 | +#### 2. Add Julia 1.10.4 |
| 106 | +``` |
| 107 | +juliaup add 1.10.4 |
| 108 | +``` |
| 109 | +#### 3. Make 1.10.4 default |
| 110 | +``` |
| 111 | +juliaup default 1.10.4 |
| 112 | +``` |
| 113 | +</details> |
| 114 | + |
| 115 | +## Package Installation |
| 116 | + |
| 117 | +You can install the package in any project with the following command : |
| 118 | + |
| 119 | +- launch julia with the command `julia` |
| 120 | +- enter the Julia package manager by typing `]` in the REPL. (the REPL should turn in blue) |
| 121 | +- if you want to activate an environment, type : `activate .` (otherwise the package will be installed in the global environment) |
| 122 | +- In order to add our unregistered package, type `add https://github.com/CRMSB/SEQ_BRUKER_A_MP2RAGE_CS_360` |
| 123 | +- if you want to use the package : `using SEQ_BRUKER_A_MP2RAGE_CS_360` |
| 124 | + |
| 125 | +## How to use the package |
| 126 | + |
| 127 | + |
| 128 | +## Version |
| 129 | + |
| 130 | + |
| 131 | +[docs-img]: https://img.shields.io/badge/docs-latest%20release-blue.svg |
| 132 | +[docs-url]: https://crmsb.github.io/SEQ_BRUKER_a_MP2RAGE_CS_360/dev/ |
| 133 | + |
| 134 | +[paper-img]: https://img.shields.io/badge/doi-10.1002/mrm.27438-blue.svg |
| 135 | +[paper-url]: https://doi.org/10.1002/mrm.27438 |
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