معرفی شرکت ها
bbrc-bx-0.5
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
BarcelonaBeta + XNAT = bx
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bbrc-bx-0.5 |
| نام | bbrc-bx |
| نسخه کتابخانه | 0.5 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Greg Operto, Jordi Huguet |
| ایمیل نویسنده | goperto@barcelonabeta.org |
| آدرس صفحه اصلی | https://gitlab.com/bbrc/xnat/bx |
| آدرس اینترنتی | https://pypi.org/project/bbrc-bx/ |
| مجوز | - |
# bx
[](https://gitlab.com/bbrc/xnat/bx/commits/master)
[](https://gitlab.com/bbrc/xnat/bx/commits/master)
[](https://pypi.org/project/bbrc-bx/)
[](https://pypi.org/project/bbrc-bx/)
[](https://pypi.org/project/bbrc-bx/)
BarcelonaBeta + XNAT = BX
The interested reader may find a description of `bx` in its native ecosystem in [J. Huguet et al.](https://www.frontiersin.org/articles/10.3389/fnins.2021.633438/full), _Frontiers in Neuroscience_ (2021) (doi:[10.3389/fnins.2021.633438](https://www.frontiersin.org/articles/10.3389/fnins.2021.633438/full)).
## Example:
## Usage
```
bx <command> <subcommand> <resource_id> --config /path/to/.xnat.cfg --dest /tmp
```
`resource_id` may be a reference to a whole XNAT project, some specific imaging
session (as found in the table returned by `bx id PROJECT_ID`) or a 'list' of
sessions (a list of existing lists may be obtained by `bx lists show`).
### **`ANTS`**:
ANTS - Advanced Normalization Tools
Available subcommands:
`files`: download all `ANTS` outputs
`snapshot`: download a snapshot from the `ANTS` pipeline
`report`: download the validation report issued by `ANTSValidator`
`tests`: creates an Excel table with all automatic tests outcomes from `ANTSValidator`
Usage:
bx ants <subcommand> <resource_id>
### **`ARCHIVING`**:
Archiving - used to collect automatic tests from `ArchivingValidator`
Available subcommands:
`tests`: creates an Excel table with all automatic tests outcomes from `ArchivingValidator`
Usage:
bx archiving <subcommand> <resource_id>
### **`ASHS`**:
ASHS (Hippocampal subfield segmentation)
Available subcommands:
`files`: download all `ASHS` outputs (segmentation maps, volumes, everything...)
`volumes`: creates an Excel table with all hippocampal subfield volumes
`snapshot`: download a snapshot from the `ASHS` pipeline
`report`: download the validation report issued by `ASHSValidator`
`tests`: creates an Excel table with all automatic tests outcomes from `ASHSValidator`
Usage:
bx ashs <subcommand> <resource_id>
### **`BAMOS`**:
BAMOS (Bayesian MOdel Selection for white matter lesion segmentation)
Available subcommands:
`files`: download all `BAMOS` outputs
`volumes`: create an Excel table with global lesion volumes
`layers`: download `layer` (i.e. depth) maps
`lobes`: download lobar segmentation maps
`stats`: create an Excel table with lesions stats per lobe and depth
`snapshot`: download a snapshot from the `BAMOS` pipeline
`report`: download the validation report issued by `BAMOSValidator`
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx bamos <subcommand> <resource_id>
References:
- Sudre et al., IEEE TMI, 2015
### **`BASIL`**:
BASIL - Bayesian Inference for Arterial Spin Labeling MRI. Arterial Spin Labeling
(ASL) MRI is a non-invasive method for the quantification of perfusion.
Available subcommands:
`perfusion`: creates an Excel table with global perfusion and arrival-time values.
`stats`: creates an Excel table with regional perfusion values (in Harvard-Oxford atlas).
`aal`: creates an Excel table with regional perfusion values (in AAL atlas).
`maps`: download the calibrated perfusion maps
`files`: download all BASIL-ASL outputs (perfusion maps, files, everything...)
`snapshot`: download a snapshot from the BASIL-ASL pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx basil <subcommand> <resource_id>
References:
- Chappell MA., IEEE Transactions on Signal Processing, 2009.
### **`BRAAK`**:
Extract morphometric/metabolic measurements based on Braak staging.
Morphometric values are based on regional volumes or cortical thickness
as estimated individually by FreeSurfer with respect to each specific stage
(namely, Braak_I_II, Braak_III_IV and Braak_V_VI). For each of them, the
mean value in all the regions related to the specific stage is returned.
Metabolic data refer to FDG update associated with each stage as defined
by their corresponding ROIs. Masks of each stage were defined based on the
CerebrA atlas (Manera et al.).
Available subcommands:
`volumes`: creates an Excel table with regional volumes for each stage
`thickness`: creates an Excel table with cortical thickness for each stage
`fdg`: creates an Excel table with the FDG uptake for each stage
Usage:
bx braak <subcommand> <resource_id>
References:
- Braak et al., Acta Neuropathol. 2006
- Schöll et al., Neuron. 2016
- Manera et al., Scientific Data. 2020
### **`CAT12`**:
CAT12 - Gray/white matter segmentation
Available subcommands:
`files`: download all `CAT12` outputs (segmentation maps, warp fields, everything...)
`volumes`: creates an Excel table with GM/WM/CSF volumes
`snapshot`: download a snapshot from the segmentation results
`report`: download the validation report issued by `CAT12Validator`
`tests`: creates an Excel table with all automatic tests outcomes from `CAT12Validator`
Usage:
bx cat12 <subcommand> <resource_id>
### **`DARTEL`**:
DARTEL - Smoothed, spatially normalized and Jacobian scaled gray matter images in MNI space
Available subcommands:
`maps`: download the MNI-normalized gray matter maps
`template`: download cohort-specific DARTEL template
`report`: download the validation report issued by `DartelNorm2MNIValidator`
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx dartel <subcommand> <resource_id>
References:
Ashburner J., Neuroimage, 2007. DOI: 10.1016/j.neuroimage.2007.07.007
### **`SPM12`**:
SPM12 - Gray/white matter segmentation
Available subcommands:
`files`: download all `SPM12` outputs (segmentation maps, warp fields, everything...)
`volumes`: creates an Excel table with GM/WM/CSF volumes
`snapshot`: download a snapshot from the segmentation results
`report`: download the validation report issued by `SPM12Validator`
`tests`: creates an Excel table with all automatic tests outcomes from `SPM12`
`rc`: downloads rc* files (DARTEL imports)
Usage:
bx spm12 <subcommand> <resource_id>
### **`DONSURF`**:
DONSURF - Diffusion ON SURFace
Available subcommands:
`files`: download all `recon-all` outputs (segmentation maps, files, everything...)
`aparc`: create an Excel table with all `aparc` measurements
`snapshot`: download a snapshot from the `recon-all` pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx donsurf <subcommand> <resource_id>
References:
- Montal V. et al., Alzheimers Dement, 2017. DOI: 10.1016/j.jalz.2017.09.013
### **`DTIFIT`**:
Processing of Diffusion-weighted Imaging data
Available subcommands:
`maps`: download parametric maps (FA, MD, AxD, RD)
`files`: download all outputs from the `DTIFIT` pipeline (up to parametric maps)
`report`: download the validation report issued by `DTIFITValidator`
`snapshot`: download a snapshot with FA map, RGB tensor and TOPUP distortion correction map
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx dtifit <subcommand> <resource_id>
### **`FREESURFER6`**:
FreeSurfer v6.0.0
Available subcommands:
`files`: download all `recon-all` outputs (segmentation maps, files, everything...)
`aseg`: create an Excel table with all `aseg` measurements
`aparc`: create an Excel table with all `aparc` measurements
hippoSfVolumes: save an Excel table with hippocampal subfield volumes
`snapshot`: download a snapshot from the `recon-all` pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx freesurfer6 <subcommand> <resource_id>
### **`FREESURFER6HIRES`**:
FreeSurfer v6.0.0 (-hires option)
Available subcommands:
`files`: download all `recon-all` outputs (segmentation maps, files, everything...)
`aseg`: create an Excel table with all `aseg` measurements
`aparc`: create an Excel table with all `aparc` measurements
hippoSfVolumes: save an Excel table with hippocampal subfield volumes
`snapshot`: download a snapshot from the `recon-all` pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx freesurfer6hires <subcommand> <resource_id>
### **`FREESURFER7`**:
FreeSurfer v7.1.1
Available subcommands:
`files`: download all `recon-all` outputs (segmentation maps, files, everything...)
`aseg`: create an Excel table with all `aseg` measurements
`aparc`: create an Excel table with all `aparc` measurements
amygNucVolumes: save an Excel table with amygdalar volumes
`brainstem`: save an Excel table with brainstem substructures volumes
`thalamus`: save an Excel table with thalamic nuclei volumes
hypothalamus: save an Excel table with hypothalamic subunits volumes
`jack`: compute the cortical AD signature with FS7 results
hippoSfVolumes: save an Excel table with hippocampal subfield volumes
`snapshot`: download a snapshot from the `recon-all` pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx freesurfer7 <subcommand> <resource_id>
### **`FREESURFER7EXTRAS`**:
FreeSurfer v7.2.0 (extra segmentation modules)
Available subcommands:
`files`: download all extra segmentation modules outputs (segmentation maps, files, everything...)
`snapshot`: download a snapshot from the extra segmentation modules pipeline
`report`: download the validation report issued by bbrc-validator
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx freesurfer7extras <subcommand> <resource_id>
### **`ID`**:
Return generic information like subject/session labels, parent project.
Usage:
bx id <resource_id>
### **`LISTS`**:
Manage experiment lists curated by BarcelonaBeta.
Available subcommands:
`show`: display all existing lists (usage: bx lists show)
Usage:
bx lists <subcommand>
### **`NIFTI`**:
Download NIfTI images from a given sequence (`SeriesDesc`).
Available subcommands:
`usable`: download `usable` images (default)
`all`: download all images found
User is then asked for sequence name (ex: T1, T2, DWI). Has to match with
the one in XNAT (wildcards accepted).
Usage:
bx nifti <subcommand> <resource_id>
### **`FDG`**:
18F-fluorodeoxyglucose PET imaging data
Available subcommands:
`landau`: creates an Excel table with the Landau's metaROI signature
`maps`: download the normalized FDG maps
`tests`: collect all automatic tests outcomes from `PetSessionValidator`
`mri`: creates an Excel table with details from associated MRI sessions
Usage:
bx fdg <subcommand> <resource_id>
Reference:
- Landau et al., Ann Neurol., 2012
### **`FTM`**:
18F-flutemetamol PET imaging data
Available subcommands:
centiloids: creates an Excel table with centiloid scales
`maps`: download the normalized FTM maps
`tests`: collect all automatic tests outcomes from `PetSessionValidator`
`mri`: creates an Excel table with details from associated MRI sessions
Usage:
bx ftm <subcommand> <resource_id>
References:
- Klunk et al, Alzheimers Dement., 2015
### **`TAU`**:
18F-RO-948 tau PET imaging data
Available subcommands:
`tests`: collect all automatic tests outcomes from `TauPetSessionValidator`
`mri`: creates an Excel table with details from associated MRI sessions
Usage:
bx tau <subcommand> <resource_id>
### **`QSMXT`**:
QSMxT - QSM processing and analysis pipeline. Quantitative susceptibility mapping
(QSM) is an MRI technique for quantifying magnetic susceptibility within biological tissue.
Available subcommands:
`stats`: creates an Excel table with regional QSM values (in FreeSurfer aseg atlas).
`maps`: download the reconstructed QSM maps
`files`: download all QSMxT outputs (QSM maps, segmentations, everything...)
`report`: download the validation report issued by `QSMxTValidator`
`tests`: create an Excel table with all automatic tests outcomes from bbrc-validator
Usage:
bx qsmxt <subcommand> <resource_id>
References:
- Stewart AW et al., Magnetic Resonance in Medicine, 2022.
### **`SCANDATES`**:
Collect acquisition dates from imaging sessions.
Usage:
bx scandates <resource_id>
### **`SIGNATURE`**:
Download composite measurements labeled as 'signatures' of Alzheimer's Disease
Available subcommands:
`jack`: based on FreeSurfer's cortical thickness and local cortical gray matter volumes
`dickerson`: based on Dickerson's cortical signatures (see references below)
Usage:
bx signature <subcommand> <resource_id>
Jack's AD signature is calculated in two versions,
weighted and not weighted. Weighted means that the formula has been
applied by normalizing each ROI value by local surface area (as explained
in the papers).
Not-weighted versions correspond to mean values across regions.
Examples:
`bx signature jack` will return Jack's signature, based on thickness and grayvol values.
`bx signature dickerson` will return AD and aging signatures, based only on
thickness values as they do not have any "grayvol" version.
References:
- Jack et al., Alzheimers Dement. 2017
- Dickerson et al., Neurology, 2011
- Bakkour et al., NeuroImage, 2013
### **`SPM12`**:
SPM12 - Gray/white matter segmentation
Available subcommands:
`files`: download all `SPM12` outputs (segmentation maps, warp fields, everything...)
`volumes`: creates an Excel table with GM/WM/CSF volumes
`snapshot`: download a snapshot from the segmentation results
`report`: download the validation report issued by `SPM12Validator`
`tests`: creates an Excel table with all automatic tests outcomes from `SPM12`
`rc`: downloads rc* files (DARTEL imports)
Usage:
bx spm12 <subcommand> <resource_id>
## Dependencies
Requires [`bbrc-pyxnat>=1.4.2`](https://gitlab.com/pyxnat/pyxnat/tree/bbrc) and
the librairies listed in `requirements.txt`.
## Install
```
pip install bbrc-bx
```
## Development
Please contact us for details on how to contribute.
[](https://www.barcelonabeta.org/)
نیازمندی
| مقدار | نام |
|---|---|
| >=1.4.2 | bbrc-pyxnat |
| >=4.5 | coverage |
| >=4.3 | lxml |
| >=2.3 | nibabel |
| >=1.16 | numpy |
| >=2.6 | openpyxl |
| >=0.24 | pandas |
| >=1.2 | pydicom |
| >=4.0 | pytest-cov |
| >=7.1 | pytest |
| >=2.21 | requests |
| >=10.1 | rich |
| >=1.10 | six |
| >=4.31 | tqdm |
| >=1.2 | xlrd |
| >=2.0 | xlutils |
| >=1.3 | xlwt |
نحوه نصب
نصب پکیج whl bbrc-bx-0.5:
pip install bbrc-bx-0.5.whl
نصب پکیج tar.gz bbrc-bx-0.5:
pip install bbrc-bx-0.5.tar.gz