From 0ec06bc63bbc17f60a9c3ce8647e3429c730bb08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yasser=20Alem=C3=A1n=20G=C3=B3mez?= Date: Thu, 29 Aug 2024 01:21:34 +0200 Subject: [PATCH] Updating the README file --- README.md | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 05ee5c3..e5384f3 100644 --- a/README.md +++ b/README.md @@ -28,11 +28,16 @@ Brief description of input options: | Option | Description | | ---------- | ------ | | `--regions`, `-r` | List available parcellations for each supra-region.| -| `--bidsdir`, `-b` | BIDs dataset folder. | -| `--derivdir`, `-d` | Derivatives folder. | +| `--bidsdir`, `-b` | BIDs dataset folder. Different BIDs directories could be entered separating them by a comma.| | `--parcodes`, `-p` | Sequence of nine one-character identifiers (one per each supra-region). | +| `--derivdir`, `-d` | Derivatives folder. Different directories could be entered separating them by a comma.| +| `--freesurferdir`, `-fr` | FreeSurfer subjects dir. If the folder does not exist it will be created.| +| `--scale`, `-s` | Scale identification. This option should be supplied for multi-resolution cortical parcellations (e.g. Lausanne or Schaeffer). | +| `--seg`, `-e` | Segmentation identifier. | +| `--nthreads`, `-n` | Number of processes to run in parallel (default= Number of cores - 4). | | `--growwm`, `-g` | Grow of GM labels inside the white matter (mm). | -| `--t1file`, `-t` | File containing the basenames of T1w images that will be ran. | +| `--subjids`, `-ids` | Subject IDs. Multiple subject ids can be specified separating them by a comma. | +| `--mergectx,`, `-mctx` | Join cortical white matter and cortical gray matter regions. | | `--force`, `-f` | Overwrite the results. | | `--verbose`, `-v` | Verbose (**0**, **1** or **2**). | | `--help`, `-h` | Help. | @@ -41,20 +46,23 @@ Brief description of input options: ##### Usage General command line to use **Chimera**: ```sh - $ python chimera_parcellation.py -b -d -p + $ chimera -b -d -p ``` +This command will run Chimera for all the subjects in the BIDs directory. + + ##### Simple examples 1. Running **Chimera** for 3 different parcellation codes (LFMFIIFIF,SFMFIIFIF,CFMFIIFIF). This will obtain the combined parcellations for all the T1-weighted images inside the BIDs dataset. ```sh - $ python chimera_parcellation.py -b -d -p LFMFIIFIF,SFMFIIFIF,CFMFIIFI + $ chimera -b -d -p LFMFIIFIF,SFMFIIFIF,CFMFIIFI ``` 2. Running **Chimera** for T1-weighted images included in a txt file: ```sh - $ python chimera_parcellation.py -b -d -p LFMFIIFIF -t + $ chimera -b -d -p LFMFIIFIF -ids ``` Example of **t1s.txt** file | sub-00001_ses-0001_run-2 @@ -63,15 +71,14 @@ Example of **t1s.txt** file 3. Cortical volumes will grow 0 and 2 mm respectively inside the white matter for the selected cortical parcellations. ```sh - $ python chimera_parcellation.py -b -d -p LFMFIIFIF -g 0,2 + $ chimera -b -d -p LFMFIIFIF -g 0,2 ``` ## Main files in the repository -1. __chimera_parcellation.py__: Main python library for performing **Chimera** parcellations. -2. __parcTypes.json__: JSON file especifying the available parcellation sources per supra-region. -3. **ANNOT_atlases** and **GCS_atlases**: Folder containing cortical atlases in *.annot* and *.gcs* file formats. -4. **mni_icbm152_t1_tal_nlin_asym_09c**: Folder containing the reference atlas used by the MIAL atlas-based thalamic parcellation method. The atlas is referenced in standard [MNI] (_Montreal Neurological Institute_) space with a high resolution T1 weighted image (__ICBM 2009c Nonlinear Asymmetric__ ). -5. **thalamic_nuclei_MIALatlas**: Folder containing the spatial probabilistic maps of 14 thalamic nuclei. +1. chimera.py__: Main python library for performing **Chimera** parcellations. +2. supraregions_dictionary.json__: JSON file especifying the available parcellation sources per supra-region. +3. **annot_atlases** and **gcs_atlases**: Folder containing cortical atlases in *.annot* and *.gcs* file formats. + #### Parcellations and methodologies for each supra-region #### 1. Cortical parcellation