合并多回声功能磁共振成像采集的多回声。
multiecho的Python项目详细描述
多回波组合
这个存储库提供了一个命令行工具来组合多回波BOLD功能磁共振成像采集的多个回波。 它目前提供了三种不同的回声消除算法：
| algorithm | description |
|---|---|
| 1. average | Echoes are weighted equally |
| 2. PAID | Echoes are weighted by their CNR, i.e. by their TE*tSNR contributions |
| 3. TE | Echoes are weighted by their TEs |
有关多回波采集和组合方案的更多信息，请参阅（例如）：
- Poser et al. (2006)。BOLD多回波EPI增强对比敏感度和减少伪影：并行获得的非均匀性脱敏功能磁共振成像。马格南。雷森。医学。55:6，第1227-35页。在
- Posse, Stefan (2012)。Multi Echo Acquisition。神经影像学62:2，第665-671页。在
Multiechois developed at the Donders Institute of the Radboud University.
安装
要安装，只需运行：
pip install multiecho
这将为您提供该软件的最新稳定版本。要获得最新版本的软件，可以直接从github源代码存储库安装包：
^{pr2}$或者，要获取最新（可能未发布）代码，请克隆此存储库并在存储库的根文件夹上运行以下命令：
pip install .
该工具只支持python3.6+。在
使用
一旦安装，名为mecombine的命令行工具将在您的路径中可用。可以通过运行mecombine -h找到详细的使用信息：
usage: combination.py [-h] [-o OUTPUTNAME] [-a {PAID,TE,average}]
[-w [WEIGHTS [WEIGHTS ...]]] [-s] [-v VOLUMES]
pattern
Combine multi-echo echoes.
Tools to combine multiple echoes from an fMRI acquisition.
It expects input files saved as NIfTIs, preferably organised
according to the BIDS standard.
Currently three different combination algorithms are supported, implementing
the following weighting schemes:
1. PAID => TE * SNR
2. TE => TE
3. Simple Average => 1
positional arguments:
pattern Globlike search pattern with path to select the echo
images that need to be combined. Because of the
search, be sure to check that not too many files are
being read
optional arguments:
-h, --help show this help message and exit
-o OUTPUTNAME, --outputname OUTPUTNAME
File output name. If not a fullpath name, then the
output will be stored in the same folder as the input.
If empty, the output filename will be the filename of
the first echo appended with a '_combined' suffix
(default: )
-a {PAID,TE,average}, --algorithm {PAID,TE,average}
Combination algorithm. Default: TE (default: TE)
-w [WEIGHTS [WEIGHTS ...]], --weights [WEIGHTS [WEIGHTS ...]]
Weights (e.g. = echo times) for all echoes (default:
None)
-s, --saveweights If passed and algorithm is PAID, save weights
(default: False)
-v VOLUMES, --volumes VOLUMES
Number of volumes that is used to compute the weights
if algorithm is PAID (default: 100)
examples:
mecombine '/project/number/bids/sub-001/func/*_task-motor_*echo-*.nii.gz'
mecombine '/project/number/bids/sub-001/func/*_task-rest_*echo-*.nii.gz' -a PAID
mecombine '/project/number/bids/sub-001/func/*_acq-MBME_*run-01*.nii.gz' -w 11 22 33 -o sub-001_task-stroop_acq-mecombined_run-01_bold.nii.gz
注意事项
当我们把所有的数据集加载到内存中时，它是无效的。我们可以迭代这些卷，并且在任何给定的时间只将最后组合的序列保存在内存中。在
将回显与PAID组合时，可能会收到运行时警告。如果数据集的体素为零，例如，如果它们被屏蔽，除以0将导致无限的权重。您可以安全地忽略此警告，但在组合后一定要检查数据。在
默认情况下，PAID将根据最后100个交易量计算权重。这是否是最佳方案有待讨论。如果你在一小部分体积上测试组合，比如说5个左右，那么权重将不稳定，你的图像可能看起来有噪音。在
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