From c1c8eafbc029c107e11a727b35bc6d8cc125721e Mon Sep 17 00:00:00 2001 From: Beliy Nikita <beliy.nikita@outlook.com> Date: Thu, 7 May 2020 11:46:10 +0200 Subject: [PATCH] replaces old bidscoin names --- example1/README.md | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/example1/README.md b/example1/README.md index 1890b85..aca22a0 100644 --- a/example1/README.md +++ b/example1/README.md @@ -23,7 +23,7 @@ ## <a name="intro"></a> Introduction This dataset is a purely fictional, designed to demonstrate the core -features of `bidscoin` bidsifier tool. +features of `bidsme` bidsifier tool. The structure of dataset is modelled of real-life dataset, currently unpublished. Several simplifications has been applied, conserving only the MRI images structure, @@ -232,7 +232,7 @@ for bidsified `.tsv` files: - `participants.json` is a sidecar json file for `participant.tsv` file, containing list of participants together with demographic information - alternative files `participants_add.json` and `participants_remove.json` are used for -demonstration of participant table manipulations by `bidscoin` +demonstration of participant table manipulations by `bidsme` - `FCsepNBack.json` is sidecar json file for task table - `VAS.json` is sidecar json file for VAS @@ -260,11 +260,11 @@ Generated bidsmap files, that can be used to bidsify this dataset are placed in - `bidsmap.yaml` must be used together with plugins - `bidsmap_noPlugin.yaml` can be used without plugins -These files can be used with `-b` option directly, or copied into `bids/code/bidscoin` directory. +These files can be used with `-b` option directly, or copied into `bids/code/bidsme` directory. #### <a name="ds_bids_plug"></a>Plugins -The plugins are stored in `resources/plugins` directory, and contains commented example of additional data management provided by `bidscoin` infrastructure. +The plugins are stored in `resources/plugins` directory, and contains commented example of additional data management provided by `bidsme` infrastructure. - `definitions.py` contains some common functions used by plugin and list of sessions and protocols used to check dataset validity - `rename_plugin.py` retrieves the demographic data and sessions names from `Appariement.xlsx`bookkeeping file @@ -286,10 +286,10 @@ In this step, a generic user-defined dataset is organized in a standardized way. To run data preparation, it will be enough to run from `example1` directory ```python -python3 bidscoin.py prepare --part-template resources/participants.json --recfolder nii=MRI --plugin resources/plugins/rename_plugin.py source/ renamed/ +python3 bidsme.py prepare --part-template resources/participants.json --recfolder nii=MRI --plugin resources/plugins/rename_plugin.py source/ renamed/ ``` -The options `--part-template resources/participants.json` will tell bidscoin to use participant json file as template for `participants.tsv` file. +The options `--part-template resources/participants.json` will tell bidsme to use participant json file as template for `participants.tsv` file. The column `participant_id` will be filled automatically, while other columns will be filled by default by `n/a`, unless they are set in plugin: @@ -299,16 +299,16 @@ session.sub_values["sex"] = "M" Without `--part-template` option the only column in participants file will be `participant_id`. -Option `--recfolder nii=MRI` will tell to `bidscoin` that image files are MRI and stored in `nii` folder. -Without this option `bidscoin` will be unable to find image files. +Option `--recfolder nii=MRI` will tell to `bidsme` that image files are MRI and stored in `nii` folder. +Without this option `bidsme` will be unable to find image files. -Option `--plugin resources/plugins/rename-plugin.py` will tell to bidscoin to load corresponding plugin. +Option `--plugin resources/plugins/rename-plugin.py` will tell to bidsme to load corresponding plugin. -Parameters `source/` and `renamed/` tells to bidscoin where to search for source dataset and where place prepared dataset. +Parameters `source/` and `renamed/` tells to bidsme where to search for source dataset and where place prepared dataset. After the execution of preparation, the `rename` folder should contain folders and files: -- **code/bidscoin**, with log files of the last execution of preparation step +- **code/bidsme**, with log files of the last execution of preparation step - **participants.tsv** and **participants.json** files with formatted and filled participant list, all columns for all subjects must be filled except `handiness`, which should contain only `n/a` - **sub-00X** folders for subjects 1-4 - **ses-HCL** sub-folders with bidsified session name (either `ses-HCL`, if run with plugin, of `ses-s01905` if run without plugin) @@ -319,17 +319,17 @@ After the execution of preparation, the `rename` folder should contain folders a This is prepared dataset, and can be modified freely at condition to conserve general structure. For example the participant table can be corrected if contain wrong or missing values. -Running bidscoin with all options can be tedious. To streamline the experience, the majority of options can be saved in configuration file by running +Running bidsme with all options can be tedious. To streamline the experience, the majority of options can be saved in configuration file by running ```python -python3 bidscoin.py -c conf.yamel --conf-save prepare <options> source/ renamed/ +python3 bidsme.py -c conf.yamel --conf-save prepare <options> source/ renamed/ ``` This will create a local `conf.yamel` file with passed options. To load the configuration: ```python -python3 bidscoin.py -c conf.yamel prepare source/ renamed/ +python3 bidsme.py -c conf.yamel prepare source/ renamed/ ``` Passing other options and using switch `--conf-save` will update configuration file. @@ -340,7 +340,7 @@ Passing other options and using switch `--conf-save` will update configuration f Bidsmap is created/tested with `map` command: ```python -python3 bidscoin.py map --plugin resources/plugins/bidsify_plugin.py --template bidsmap_template.yaml renamed/ bids/ +python3 bidsme.py map --plugin resources/plugins/bidsify_plugin.py --template bidsmap_template.yaml renamed/ bids/ ``` The option `--plugin resources/plugins/bidsify_plugin.py` will load correspondent plugin (the used plugin is the same as for bidsification to ensure that all modifications needed to @@ -353,10 +353,10 @@ The `bidsmap_template.yaml` works with example dataset, but for real data a diff The parameters `renamed/` and `bids/` tells where prepared dataset is stored and where the bidsified dataset will be placed. First execution of `map` usually results into huge amount of warnings and occasional errors. -These warnings and errors must be corrected. The details of various warnings and corrections to apply can be found in `bidscoin` documentation. +These warnings and errors must be corrected. The details of various warnings and corrections to apply can be found in `bidsme` documentation. The working bidsmap can be found in `resources/map` directory. -If placed in `bids/code/bidscoin/` directory, the `map` should not produce any warnings. +If placed in `bids/code/bidsme/` directory, the `map` should not produce any warnings. @@ -372,7 +372,7 @@ For example `resources/plugins/process_plugin.py` fills the `nandiness` column, fMRI and diffusion images in single 4D image. ```python -python3 bidscoin.py process --plugin resources/plugins/process_plugin.py renamed/ bids/ +python3 bidsme.py process --plugin resources/plugins/process_plugin.py renamed/ bids/ ``` After running, the column `handiness` must be filled and fMRI files @@ -380,7 +380,7 @@ After running, the column `handiness` must be filled and fMRI files must be merged in one file. This step can be easily replaced by any custom script and/or pipeline. The only advantage -is some `bids` and `bidscoin` specific checks and recording identification. +is some `bids` and `bidsme` specific checks and recording identification. ### <a name="run_bids"></a>Bidsification step @@ -388,7 +388,7 @@ is some `bids` and `bidscoin` specific checks and recording identification. The final step is bidsification, it is run with `bidsify` command: ```python -python3 bidscoin.py map --plugin resources/plugins/bidsify_plugin.py renamed/ bids/ +python3 bidsme.py map --plugin resources/plugins/bidsify_plugin.py renamed/ bids/ ``` The `--plugin resources/plugins/bidsify_plugin.py` option loads an @@ -400,7 +400,7 @@ The bidsified dataset should be found in `bids/` folder and should be fully bids complaint, including the participant and scans json sidecar files and json files with exported scans meta-data. -`bidscoin` offer the possibility to rename subjects during bidsification. +`bidsme` offer the possibility to rename subjects during bidsification. To do so, it will be enough to change value of `scan.subject` in `ParticipantEP` function, as demonstrated in `plugin resources/plugins/bidsify_plugin.py` file on lines 85--89. -- GitLab