Adding Gadgetron noise adjustment example to docs

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-ARG DEVCONTAINER_BASE=mcr.microsoft.com/devcontainers/base:1.0.9-ubuntu-22.04
+ARG DEVCONTAINER_BASE=mcr.microsoft.com/devcontainers/base:2.1.5-ubuntu24.04
 
 FROM ${DEVCONTAINER_BASE} AS devcontainer
 

docs/reference/gadgetron/gadgetron.md

@@ -1,4 +1,4 @@
-# Gadgeton examples
+# Gadgetron examples
 
 [Gadgetron](https://github.com/gadgetron/gadgetron) is an open source project
 for medical image reconstruction and can be used with Tyger. These examples
@@ -16,7 +16,7 @@ This will generate a `testdata.h5` file. You can then run a reconstruction with:
 
 ```bash
 ismrmrd_hdf5_to_stream -i testdata.h5 --use-stdout \
-| tyger run exec -f  basic_gadgetron.yml \
+| tyger run exec -f basic_gadgetron.yml \
 | ismrmrd_stream_to_hdf5 --use-stdin -o out_basic.h5
 ```
 
@@ -26,6 +26,65 @@ ismrmrd_hdf5_to_stream -i testdata.h5 --use-stdout \
 <!--@include: ./basic_gadgetron.yml-->
 ```
 
+## Using dependent measurements
+
+It is common in MRI to perform a noise reference scan before the main scan. The
+noise scan is used to estimate a noise covariance matrix and the subsequent scan
+is reconstructed after noise pre-whitening using this covariance matrix.
+
+For this example, download the noise and main scan raw data files:
+
+```bash
+curl -OL https://aka.ms/tyger/docs/samples/dependencies/noise_scan.h5
+curl -OL https://aka.ms/tyger/docs/samples/dependencies/main_scan.h5
+```
+
+### Compute noise covariance matrix
+
+Start by creating buffers for the noise data and covariance matrix:
+
+```bash
+noise_buffer_id=$(tyger buffer create)
+noise_covariance_buffer_id=$(tyger buffer create)
+```
+
+Then write the noise data to the buffer:
+
+```bash
+ismrmrd_hdf5_to_stream -i noise_scan.h5 --use-stdout \
+    | tyger buffer write $noise_buffer_id
+```
+
+Now compute the noise covariance matrix using the two buffers:
+
+```bash
+tyger run exec -f noise_gadgetron.yml \
+    -b input=$noise_buffer_id \
+    -b noisecovariance=$noise_covariance_buffer_id
+```
+
+`noise_gadgetron.yml` looks like this:
+```yaml
+<!--@include: ./noise_gadgetron.yml-->
+```
+
+### Reconstruction
+
+We are ready to reconstruct the main scan data by referencing the noise
+covariance matrix buffer:
+
+```bash
+ismrmrd_hdf5_to_stream -i main_scan.h5 --use-stdout \
+    | tyger run exec -f snr_gadgetron.yml --logs -b noisecovariance=$noise_covariance_buffer_id  \
+    | ismrmrd_stream_to_hdf5 --use-stdin -o main-scan-recon.h5
+```
+
+
+`snr_gadgetron.yml` looks like this (note the two input buffers):
+```yaml
+<!--@include: ./snr_gadgetron.yml-->
+```
+
 ## Distributed reconstruction
 
 Next is an example that uses a distributed run. First, download the raw data:
@@ -38,7 +97,7 @@ Then run:
 
 ```bash
 ismrmrd_hdf5_to_stream -i binning.h5 --use-stdout \
-| tyger run exec -f  distributed_gadgetron.yml --logs \
+| tyger run exec -f distributed_gadgetron.yml --logs \
 | ismrmrd_stream_to_hdf5 --use-stdin -o out_binning.h5
 ```
 

docs/reference/gadgetron/noise_gadgetron.yml

@@ -0,0 +1,20 @@
+job:
+  codespec:
+    image: ghcr.io/gadgetron/gadgetron/gadgetron_ubuntu_rt_nocuda:latest
+    buffers:
+      inputs:
+        - input
+      outputs:
+        - noisecovariance
+    args:
+      - "-c"
+      - "default_measurement_dependencies.xml"
+      - "--from_stream"
+      - "-i"
+      - "$(INPUT_PIPE)"
+      - "-o"
+      - /dev/null
+      - --disable_storage
+      - 'true'
+      - --parameter
+      - noisecovarianceout=$(NOISECOVARIANCE_PIPE)

docs/reference/gadgetron/snr_gadgetron.yml

@@ -0,0 +1,21 @@
+job:
+  codespec:
+    image: ghcr.io/gadgetron/gadgetron/gadgetron_ubuntu_rt_nocuda:latest
+    buffers:
+      inputs:
+        - input
+        - noisecovariance
+      outputs:
+        - output
+    args:
+      - "-c"
+      - "Generic_Cartesian_FFT.xml"
+      - "--from_stream"
+      - "-i"
+      - "$(INPUT_PIPE)"
+      - "-o"
+      - "$(OUTPUT_PIPE)"
+      - --disable_storage
+      - 'true'
+      - --parameter
+      - noisecovariancein=$(NOISECOVARIANCE_PIPE)