From c4bba8c2623a97d4fcf67da9e1aa2fcd6fff3adb Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:09:00 -0400 Subject: [PATCH 1/8] README: Fix "team" header --- README.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/README.md b/README.md index 660b90ed..9070b6bb 100644 --- a/README.md +++ b/README.md @@ -242,7 +242,7 @@ To report any bugs or issues, see [the Issues tool on the PyDesigner GitHub page PyDesigner is a joint collarobation and as such consists of several developers. -### Developer +### Developers @@ -253,7 +253,6 @@ PyDesigner is a joint collarobation and as such consists of several developers. Medical University of South Carolina< dhiman@musc.edu -### Developer @@ -264,7 +263,6 @@ PyDesigner is a joint collarobation and as such consists of several developers. Medical University of South Carolina teves@musc.edu -### From 826c24265e6536ae496828ba7356fce2c2f7ead5 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:13:50 -0400 Subject: [PATCH 2/8] README: Add `--adv` flag info --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 9070b6bb..362e4ffc 100644 --- a/README.md +++ b/README.md @@ -231,6 +231,7 @@ python /Path/to/pydesigner.py --denoise --degibbs --smooth --rician --mask --top `--o` - specifies output folder
`--verbose` - prints out all output
`--force` - overwrites existing files in output folder
+`--adv` - disables safety checks for advanced users who want to force a preprocessing step. **WARNING: FOR ADVANCED USERS ONLY**
## Questions and Issues From 6764ea7d14c7f4ccb8c5e90acafcdd68e6f0b956 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:38:34 -0400 Subject: [PATCH 3/8] README: Change flag section to table --- README.md | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 362e4ffc..4caefa8c 100644 --- a/README.md +++ b/README.md @@ -220,18 +220,22 @@ python /Path/to/pydesigner.py --denoise --degibbs --smooth --rician --mask --top **Basic PyDesigner Flags** -`--standard` - runs the standard pipeline (denoising, gibbs unringing, topup + eddy, b1 bias correction, CSF-excluded smoothing, rician bias correction, normalization to white matter in the first B0 image, IRWLLS, CWLLS DKI fit, outlier detection and removal)
-`--denoise` - performs denoising
-`--degibbs` - performs gibbs unringing correction
-`--smooth` - performs smoothing
-`--rician` - performs rician bias correction
-`--mask` - computes brain mask prior to tensor fitting; recommended
-`--undistort` - performs image undistortion via FSL eddy
-`--topup` - incorporates top up B0 series; required for `--undistort`
-`--o` - specifies output folder
-`--verbose` - prints out all output
-`--force` - overwrites existing files in output folder
-`--adv` - disables safety checks for advanced users who want to force a preprocessing step. **WARNING: FOR ADVANCED USERS ONLY**
+ | Flag | Description | + | :---------- | :- | + |`--standard` | runs the standard pipeline (denoising, gibbs unringing, topup + eddy, b1 bias correction, CSF-excluded smoothing, rician bias correction, normalization to white matter in the first B0 image, IRWLLS, CWLLS DKI fit, outlier detection and removal) | + |`--denoise` |performs denoising| + |`--degibbs` |performs gibbs unringing correction| + |`--smooth` |performs smoothing| + |`--rician` |performs rician bias correction| + |`--mask` |computes brain mask prior to tensor fitting; recommended| + |`--undistort`|performs image undistortion via FSL eddy| + |`--topup` | performs EPI correction byincorporating topup B0 series; required for `--undistort`| + |`--o` |specifies output folder| + |`--force` |overwrites existing files in output folder| + |`--resume` |resumes processing from a previous state; only if same output folder| + |`--verbose` |prints out all output: recommended for debugging| + |`--adv` |disables safety checks for advanced users who want to force a preprocessing step. **WARNING: FOR ADVANCED USERS ONLY**| + ## Questions and Issues From 2392899ccac7e1b7fac6a203d279079f17eb8847 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:46:43 -0400 Subject: [PATCH 4/8] README: Format table --- README.md | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 4caefa8c..4fa6ef37 100644 --- a/README.md +++ b/README.md @@ -218,23 +218,25 @@ python /Path/to/pydesigner.py --denoise --degibbs --smooth --rician --mask --top **Note**: Using `--undistort` and `--topup` without supplying top up data will return an error. -**Basic PyDesigner Flags** +### Basic PyDesigner Flags + +Flags are to be preceeded by `--`. For example, to parse a _denoise_ flag, one would type the flag as `--denoise`. | Flag | Description | | :---------- | :- | - |`--standard` | runs the standard pipeline (denoising, gibbs unringing, topup + eddy, b1 bias correction, CSF-excluded smoothing, rician bias correction, normalization to white matter in the first B0 image, IRWLLS, CWLLS DKI fit, outlier detection and removal) | - |`--denoise` |performs denoising| - |`--degibbs` |performs gibbs unringing correction| - |`--smooth` |performs smoothing| - |`--rician` |performs rician bias correction| - |`--mask` |computes brain mask prior to tensor fitting; recommended| - |`--undistort`|performs image undistortion via FSL eddy| - |`--topup` | performs EPI correction byincorporating topup B0 series; required for `--undistort`| - |`--o` |specifies output folder| - |`--force` |overwrites existing files in output folder| - |`--resume` |resumes processing from a previous state; only if same output folder| - |`--verbose` |prints out all output: recommended for debugging| - |`--adv` |disables safety checks for advanced users who want to force a preprocessing step. **WARNING: FOR ADVANCED USERS ONLY**| + |`standard` | runs the standard pipeline (denoising, gibbs unringing, topup + eddy, b1 bias correction, CSF-excluded smoothing, rician bias correction, normalization to white matter in the first B0 image, IRWLLS, CWLLS DKI fit, outlier detection and removal) | + |`denoise` |performs denoising| + |`degibbs` |performs gibbs unringing correction| + |`smooth` |performs smoothing| + |`rician` |performs rician bias correction| + |`mask` |computes brain mask prior to tensor fitting; recommended| + |`undistort`|performs image undistortion via FSL eddy| + |`topup` | performs EPI correction byincorporating topup B0 series; required for `--undistort`| + |`o` |specifies output folder| + |`force` |overwrites existing files in output folder| + |`resume` |resumes processing from a previous state; only if same output folder| + |`verbose` |prints out all output: recommended for debugging| + |`adv` |disables safety checks for advanced users who want to force a preprocessing step. **WARNING: FOR ADVANCED USERS ONLY**| ## Questions and Issues From b35775f1ead54e75204139007c47e627915dfd48 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:47:04 -0400 Subject: [PATCH 5/8] README: Header and TOC update --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4fa6ef37..ff950b0c 100644 --- a/README.md +++ b/README.md @@ -52,6 +52,9 @@ This is a collaboration project between MUSC and NYU to bring easy-to-use dMRI p **[L- Python](#python)**
**[L- PyDesigner](#pydesigner)**
**[Running PyDesigner](#running-pydesigner)**
+**[L- Before Running PyDesigner](#before-running-pydesigner)**
+**[L- To Run PyDesigner](#to-run-pydesigner)**
+**[L- Basic PyDesigner Flags](#basic-pydesigner-flags)**
**[Meet the Team](#meet-the-team)**
## General Information @@ -186,13 +189,13 @@ PyDesigner is located here: `/PyDesigner-master/designer/pydesigner.py` ## Running PyDesigner -**Before Running PyDesigner** +### Before Running PyDesigner Ensure that all your DICOMS are converted to NifTi files and that all diffusion series have a valid `.json` file, as well as `.bvec` and `.bval` files where applicable. Dicom to nifti conversion can be done with [dcm2niix available for download here](https://github.com/rordenlab/dcm2niix). Ensure that none of your file or folder names contain a period (aside from the file extension; eg. DKI.nii). -**To Run PyDesigner** +### To Run PyDesigner Switch to the appropriate conda environment; run `conda activate dmri` if you followed this guide. Then, for any given subject, call PyDesigner with the relevant flags: From 0dd0b4e3fa749a6ee576be8948e1a106692ca410 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:51:17 -0400 Subject: [PATCH 6/8] README: Improve TOC readibility --- README.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index ff950b0c..af04f0dc 100644 --- a/README.md +++ b/README.md @@ -43,18 +43,18 @@ This is a collaboration project between MUSC and NYU to bring easy-to-use dMRI p **[General Information](#general-information)**
**[Introduction](#introduction)**
**[L- The PyDesigner Pipeline](#the-pydesigner-pipeline)**
-**[L-- Image Acquisition](#image-acquisition)**
-**[L-- Preprocessing](#preprocessing)**
-**[L-- Tensor Estimation](#tensor-estimation)**
+**[L-- _Image Acquisition_](#image-acquisition)**
+**[L-- _Preprocessing_](#preprocessing)**
+**[L-- _Tensor Estimation_](#tensor-estimation)**
**[Installation](#installation)**
-**[L- FSL](#fsl)**
-**[L- MRTRIX3](#mrtrix3)**
-**[L- Python](#python)**
-**[L- PyDesigner](#pydesigner)**
+**[L- _FSL_](#fsl)**
+**[L- _MRTRIX3_](#mrtrix3)**
+**[L- _Python_](#python)**
+**[L- _PyDesigner_](#pydesigner)**
**[Running PyDesigner](#running-pydesigner)**
-**[L- Before Running PyDesigner](#before-running-pydesigner)**
-**[L- To Run PyDesigner](#to-run-pydesigner)**
-**[L- Basic PyDesigner Flags](#basic-pydesigner-flags)**
+**[L- _Before Running PyDesigner_](#before-running-pydesigner)**
+**[L- _To Run PyDesigner_](#to-run-pydesigner)**
+**[L- _Basic PyDesigner Flags_](#basic-pydesigner-flags)**
**[Meet the Team](#meet-the-team)**
## General Information From e2edd956a81007a4db3d695d32533e6741e0ff91 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:51:40 -0400 Subject: [PATCH 7/8] README: Update project cycle --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index af04f0dc..6dcd0c61 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ -# PyDesigner [UNDER CONSTRUCTION] -**Project is currently under construction and will not run. Official release will be marked by the removal of 'under construction' header.** +# PyDesigner [DEVELOPMENTAL CYCLE] +**Project is currently under developmental cycle and is undergoing stability testing and debugging. Users are recommended to wait for a stable public release instead.** **_Disclaimer:_** ``` -This project is in very early stages of development and most likely will not work as intended. +This project is in early stages of development and most likely will not work as intended. We are not responsible for any data corruption, loss of valuable data, computer issues, you getting fired because you chose to run this, or a thermonuclear war. We strongly encourage all potential users to wait for an official release. From fda609ee88bd92df56c2b2fcb8a2b0c72d4f4f73 Mon Sep 17 00:00:00 2001 From: Siddhartha Dhiman Date: Tue, 22 Oct 2019 10:59:53 -0400 Subject: [PATCH 8/8] README: Update disclaimer --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6dcd0c61..3c3ec6dd 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,9 @@ This project is in early stages of development and most likely will not work as intended. We are not responsible for any data corruption, loss of valuable data, computer issues, you getting fired because you chose to run this, or a thermonuclear war. We strongly encourage -all potential users to wait for an official release. +all potential users to wait for an official release. Ina ll seriousness, do NOT used this for +any data analysis, speculation, or writing papers: 1) not all citations have been incorporated, +and 2) this is a developmental cycle with no papers to cite back on. ```

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