Installation instructions

The README.md file now includes installation instructions

README.md

@@ -3,16 +3,34 @@ Converts physio data from a CMRR DICOM file to BIDS physiological recording
 
 ## Usage
 ```
-python dcm2bidsphysio.py --infile <DCMfile>      \
-                         --bidsprefix <Prefix>
+dcm2bidsphysio --infile <DCMfile> --bidsprefix <Prefix>
 ```
 
 Example:
 ```
-python dcm2bidsphysio.py --infile 07+epi_MB4_2mm_Physio+00001.dcm      \
-                         --bidsprefix BIDSfolder/sub-01/func/sub-01_task-REST_run-1
+dcm2bidsphysio --infile 07+epi_MB4_2mm_Physio+00001.dcm      \
+                           --bidsprefix BIDSfolder/sub-01/func/sub-01_task-REST_run-1
 ```
 
+## Arguments
+ * `<DCMfile>` is the DICOM file that contains the physiological recordings.
+ * `<Prefix>` is the prefix that will be used for the BIDS physiology files.  The script will save the files: `<Prefix>_recording-<label>_physio.json` and `<Prefix>_recording-<label>_physio.tsv.gz`, with labels `cardiac` and `respiratory` (if present in the `DCMfile`).
+
+Note: If desired, you can use the corresponding `_bold.nii.gz` BIDS file as `--bidsprefix`. The script will strip the `_bold.nii.gz` part from the filename and use what is left as `<Prefix>`. This way, you can assure that the output physiology files match the `_bold.nii.gz` file for which they are intended.
+
+## Installation
+You can install the tool by downloading the package and installing it
+with `pip`:
+
+```
+mkdir /tmp/dcm2bidsphysio && \
+    curl -sSL https://github.com/cbinyu/dcm2bidsphysio/archive/master.tar.gz \
+        | tar -vxz -C /tmp/dcm2bidsphysio --strip-components=1 && \
+    cd /tmp/dcm2bidsphysio && \
+    pip install . && \
+    cd / && \
+    rm -rf /tmp/dcm2bidsphysio
+```
 
 ## Docker usage
 ```
@@ -34,9 +52,3 @@ docker run --rm \
 ```
 
 
-## Arguments
- * `<DCMfile>` is the DICOM file that contains the physiological recordings.
- * `<Prefix>` is the prefix that will be used for the BIDS physiology files.  The script will save the files: `<Prefix>_recording-<label>_physio.json` and `<Prefix>_recording-<label>_physio.tsv.gz`, with labels `cardiac` and `respiratory` (if present in the `DCMfile`).
-
-Note: If desired, you can use the corresponding `_bold.nii.gz` BIDS file as `--bidsprefix`. The script will strip the `_bold.nii.gz` part from the filename and use what is left as `<Prefix>`. This way, you can assure that the output physiology files match the `_bold.nii.gz` file for which they are intended.
-