Merge branch 'pride-svr-0.2.0'

SVRTK · Apr 6, 2022 · ab5bff7 · ab5bff7
2 parents e34261f + 9c78a32
commit ab5bff7
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Showing 6 changed files with 20 additions and 16 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.idea
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ Minimum hardware requirements:
  - CPU with 6 cores
  - 16 GB RAM
  - For GPU-accelerated reconstruction: Nvidia GPU with 12GB video memory
- - At least 30GB free disk space 
+ - At least 30GB free disk space
 
 Recommended hardware requirements:
 - CPU with ≥10 cores
@@ -58,12 +58,12 @@ git clone --recurse-submodules https://github.com/SVRTK/svrtk-docker-gpu.git /ho
 ### Option 1 --- Install using pre-built Docker image
 #### 1.1 Download the pre-built Docker image from DockerHub:
 ```
-docker pull fetalsvrtk/svrtk:svrtk-docker-gpu-0.10
+docker pull fetalsvrtk/svrtk:pride-svr-docker-0.2.0
 ```
 #### 1.2 Test the Docker container is working:
 
 ```
-docker run -it fetalsvrtk/svrtk:svrtk-docker-gpu-0.10
+docker run -it fetalsvrtk/svrtk:pride-svr-docker-0.2.0
 ```
 Once inside the container, test MIRTK is working by running:
 
@@ -96,13 +96,13 @@ wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/checkpoin
 #### 2.3 Build the container using the Dockerfile:
 
 ```
-docker build -f svrtk-docker-gpu.Dockerfile -t fetalsvrtk/svrtk:svrtk-docker-gpu-0.10 .
+docker build -f svrtk-docker-gpu.Dockerfile -t fetalsvrtk/svrtk:pride-svr-docker-0.2.0 .
 ```
 
 #### 2.4 Test the Docker container is working:
 
 ```
-docker run -it fetalsvrtk/svrtk:svrtk-docker-gpu-0.10
+docker run -it fetalsvrtk/svrtk:pride-svr-docker-0.2.0
 ```
 Once inside the container, test MIRTK is working by running:
 
@@ -122,7 +122,7 @@ Copy nifti files (labelled `stack1.nii.gz`, `stack2.nii.gz`, ... `stackN.nii.gz`
 Then:
 
 ```
-docker run -v "svrtk-docker-gpu/recon":/home/recon fetalsvrtk/svrtk:svrtk-docker-gpu-0.10 /home/scripts/docker-recon-brain-auto.bash /home/recon
+docker run -v "svrtk-docker-gpu/recon":/home/recon fetalsvrtk/svrtk:pride-svr-docker-0.2.0 /home/scripts/docker-recon-brain-auto.bash /home/recon
 ```
 
 This will output a 3D SVR-reconstructed volume named `SVR-output.nii.gz`.
@@ -131,5 +131,5 @@ This will output a 3D SVR-reconstructed volume named `SVR-output.nii.gz`.
 ##### Optional:
 If you have successfully installed CUDA, you can run the GPU-accelerated version with:
 ```
-docker run -it --gpus all -v "svrtk-docker-gpu/recon":/home/recon fetalsvrtk/svrtk:svrtk-docker-gpu-0.10 /home/scripts/docker-recon-brain-auto.bash /home/recon
-```
+docker run -it --gpus all -v "svrtk-docker-gpu/recon":/home/recon fetalsvrtk/svrtk:pride-svr-docker-0.2.0 /home/scripts/docker-recon-brain-auto.bash /home/recon
+```
diff --git a/recon/pride/SVR/StartSVR.bat b/recon/pride/SVR/StartSVR.bat
@@ -4,7 +4,7 @@
 
 :: Docker image name (default: svrtk-docker-gpu)
 set hostName=%COMPUTERNAME%
-set "dockerImageName=fetalsvrtk/svrtk:svrtk-docker-gpu-0.10"
+set "dockerImageName=fetalsvrtk/svrtk:pride-svr-docker-0.2.0"
 ECHO Using Docker Image: %dockerImageName%
 
 :: Clear TempOutputSeries
@@ -46,4 +46,4 @@ if "%hostName%" EQU "PRIDESVR02-PC" (
 :: Clean Recon Directory
 ECHO Cleaning recon directory ...
 powershell.exe C:\svrtk-docker-gpu\scripts\reconDirClean.bat
-ECHO DONE
+ECHO DONE
diff --git a/recon/pride/SVR/StartSVR_GPU.bat b/recon/pride/SVR/StartSVR_GPU.bat
@@ -4,7 +4,7 @@
 
 :: Docker image name (default: svrtk-docker-gpu)
 set hostName=%COMPUTERNAME%
-set "dockerImageName=fetalsvrtk/svrtk:svrtk-docker-gpu-0.10"
+set "dockerImageName=fetalsvrtk/svrtk:pride-svr-docker-0.2.0"
 ECHO Using Docker Image: %dockerImageName%
 
 :: Clear TempOutputSeries
@@ -46,4 +46,4 @@ if "%hostName%" EQU "PRIDESVR02-PC" (
 :: Clean Recon Directory
 ECHO Cleaning recon directory ...
 powershell.exe C:\svrtk-docker-gpu\scripts\reconDirClean.bat
-ECHO DONE
+ECHO DONE
diff --git a/scripts/StartSVR.bash b/scripts/StartSVR.bash
@@ -5,8 +5,8 @@
 # Admin
 userName=$USER
 
-# Docker image name (default: svrtk-docker-gpu)
-dockerImageName=fetalsvrtk/svrtk:svrtk-docker-gpu
+# Docker image name
+dockerImageName=fetalsvrtk/svrtk:pride-svr-docker-0.2.0
 dockerImageFolderName=svrtk-docker-gpu
 echo "Using Docker Image:" $dockerImageName
 

diff --git a/scripts/svr_nii2pridedcm.py b/scripts/svr_nii2pridedcm.py
@@ -64,6 +64,8 @@
     0x2001101a: ('FL', '3', "PC Velocity", '', 'PCVelocity'),
     0x2001101d: ('IS', '1', "Reconstruction Number MR", '', 'ReconstructionNumberMR'),
     0x20051035: ('CS', '1', '', '', 'unknowntag20051035'), # PIXEL --- this seems to also correspond to MRSeriesDataType?
+    0x20051011: ('CS', '1', 'MR Image Type', '', 'MRImageType'),
+    0x2005106e: ('CS', '1', 'MR Scan Sequence', '', 'MRScanSequence'),
 
     # Philips "Stack" Tags
     0x2001105f: ('SQ', '1','Stack','','Stack'),
@@ -463,7 +465,8 @@ def elem_initialise(uid_instance, uid_series_instance, uid_frame_of_reference, n
         'NumberOfStacks': 1,
         'ReconstructionNumberMR': 2,
         'NumberOfDynamicScans': 1,
-
+        'MRImageType': 'M',
+        'MRScanSequence': 'SE',
     }
 
     return elements_to_define_meta, elements_to_transfer_meta, elements_to_define_ds, elements_to_transfer_ds, non_std_elements_to_define_ds
@@ -564,7 +567,7 @@ def create_seq_stack():
 
     # override elements
     setattr(ds, 'SeriesNumber', str(int(str(getattr(dcmIn, 'SeriesNumber'))) + 1) ) # +1 to SeriesNumber
-    # setattr(ds, 'AcquisitionNumber', str(getattr(dcmIn, 'AcquisitionNumber')))
+    setattr(ds, 'AcquisitionNumber', str(getattr(dcmIn, 'SeriesNumber'))[:-2])
     # setattr(ds, 'InstanceCreationDate', str(today_date) )
     # setattr(ds, 'InstanceCreationTime', str(today_time) )
     # setattr(ds, 'SeriesDate', str(today_date) )