Multiple fixes

- Pull in latest code changes at MRtrix3/mrtrix3#3011 to ensure no regression has occurred in fixing other issues. - Fix invocation of peakscheck for dwi2tensor outputs. - Fix container entrypoint. - Fix README to include invocation of container and reflect fix to container entrypoint.
Lestropie · Nov 17, 2024 · 41dff10 · 41dff10
1 parent 967025f
commit 41dff10
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Showing 6 changed files with 32 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -18,8 +18,8 @@ RUN apt-get -qq update \
 
 FROM mrtrix3-builder AS mrtrix3-eval-builder
 # Version of MRtrix3 to be evaluated
-# This is branch "dwi_metadata_master" as at 2024-09-19
-ARG MRTRIX3_GIT_COMMITISH="01a09b8985568b52ad81fd1a499c3feab872881b"
+# This is branch "dwi_metadata_master" as at 2024-11-16
+ARG MRTRIX3_GIT_COMMITISH="fc0e8f144b161a594eda733ebc9cb4eb6b72e8cb"
 #ARG MRTRIX3_GIT_COMMITISH="dwi_metadata_master"
 # Command-line arguments for `./configure`
 ARG MRTRIX3_CONFIGURE_FLAGS="-nogui"
@@ -146,4 +146,5 @@ ENV FSLDIR="/opt/fsl" \
     FSLWISH="/opt/fsl/bin/fslwish" \
     PATH="/opt/mrtrix3/bin:/opt/peakscmds/build/bin:/opt/dcm2niix/build/bin:/opt/fsl/share/fsl/bin:$PATH"
 
-CMD ["/main.py"]
+ENTRYPOINT ["/main.py"]
+
diff --git a/README.md b/README.md
@@ -11,13 +11,14 @@ This can be done via eg.:
 ```ShellSession
 docker build . -t dwi_metadata:latest
 mkdir scratch
-docker run -it --rm -v $(pwd)/scratch:/scratch /main.py /data /scratch /scratch/log.log
+docker run -it --rm -v $(pwd)/scratch:/scratch dwi_metadata:latest /data /scratch /scratch/log.log
 ```
 
-The `main.py` script currently expects all relevant commands to be present in `PATH`.
+The execution scripts expect all relevant commands to be present in `PATH`.
 This includes the `peakscheck` and `peaksconvert` commands proposed for *MRtrix3*,
 which currently necessitates installation of the following branch:
-https://github.com/MRtrix3/mrtrix3/pull/2918
+https://github.com/MRtrix3/mrtrix3/pull/2918.
+The container environment ensures that this is all set up as required.
 
 ## Software dependencies
 

diff --git a/dwi_metadata/fsl/fsl.py b/dwi_metadata/fsl/fsl.py
@@ -14,7 +14,11 @@ def execute(inputname, inputdir, maskdir, scratchdir):
         dtifit.run(inputdir, maskdir, dtifitdir)
         conversiondir = op.join(scratchdir, f'dtifit_{op.basename(inputdir)}_to_scannerspace')
         dtifit.convert(dtifitdir, conversiondir)
-        tests.peaks(f'FSL dtifit from {inputname}', conversiondir, maskdir, 'nii')
+        tests.peaks(f'FSL dtifit from {inputname}',
+                    conversiondir,
+                    maskdir,
+                    'mif',
+                    'nii')
     execute('dcm2niix',
             op.join(scratchdir, 'dcm2niix'),
             op.join(scratchdir, 'mask_dcm2niix'),
@@ -39,10 +43,18 @@ def execute(inputname, inputdir, maskdir, scratchdir):
         bedpostx.run(inputdir, maskdir, bedpostxdir)
         conversiondir = op.join(scratchdir, f'bedpostx_from_{op.basename(inputdir)}_sph2peaks')
         bedpostx.convert(bedpostxdir, conversiondir, False)
-        tests.peaks(f'bedpostx from {inputname}; spherical coordinates', conversiondir, maskdir, 'nii')
+        tests.peaks(f'bedpostx from {inputname}; spherical coordinates',
+                    conversiondir,
+                    maskdir,
+                    'mif',
+                    'nii')
         conversiondir = op.join(scratchdir, f'bedpostx_from_{op.basename(inputdir)}_dyads2peaks')
         bedpostx.convert(bedpostxdir, conversiondir, True)
-        tests.peaks(f'bedpostx from {inputname}; 3-vectors', conversiondir, maskdir, 'nii')
+        tests.peaks(f'bedpostx from {inputname}; 3-vectors',
+                    conversiondir,
+                    maskdir,
+                    'mif',
+                    'nii')
     execute('dcm2niix',
             op.join(scratchdir, 'dcm2niix'),
             op.join(scratchdir, 'mask_dcm2niix'),

diff --git a/dwi_metadata/mrtrix3/dwi2tensor.py b/dwi_metadata/mrtrix3/dwi2tensor.py
@@ -32,7 +32,7 @@ def run(indir, extensions, maskdir, dwi2tensordir):
                        + grad_option,
                        check=True)
         subprocess.run(['tensor2metric', tensor_image_path,
-                        '-vector', op.join(dwi2tensordir, f'{v}_vector.{extensions[0]}'),
+                        '-vector', op.join(dwi2tensordir, f'{v}.{extensions[0]}'),
                         '-mask', mask_path,
                         '-modulate', 'fa',
                         '-quiet'],

diff --git a/dwi_metadata/mrtrix3/mrtrix3.py b/dwi_metadata/mrtrix3/mrtrix3.py
@@ -115,6 +115,7 @@ def test_dwi2tensor(scratchdir):
     tests.peaks(f'MRtrix3 dwi2tensor from dcm2niix',
                 op.join(scratchdir, 'dwi2tensor_from_dcm2niix'),
                 op.join(scratchdir, 'mask_dcm2niix'),
+                'nii',
                 'nii')
     for extensions, reorient in tqdm(itertools.product(EXTENSIONS, (False, True)),
                                      desc='Running MRtrix3 dwi2tensor on MRtrix3 mrconvert outputs',
@@ -126,5 +127,9 @@ def test_dwi2tensor(scratchdir):
                        extensions,
                        maskdir,
                        outdir)
-        tests.peaks(f'MRtrix3 dwi2tensor from mrconvert {version_string}', outdir, maskdir, extensions[0])
+        tests.peaks(f'MRtrix3 dwi2tensor from mrconvert {version_string}',
+                    outdir,
+                    maskdir,
+                    extensions[0],
+                    extensions[0])
 
diff --git a/dwi_metadata/tests.py b/dwi_metadata/tests.py
@@ -179,7 +179,7 @@ def metadata(testname, inputdir, file_extensions):
 
 
 
-def peaks(testname, inputdir, maskdir, mask_extension):
+def peaks(testname, inputdir, maskdir, image_extension, mask_extension):
     errors = []
     logger.info(f'Verifying peak orientations for {testname}')
     for v in tqdm(VARIANTS, desc=f'Verifying peak orientations for {testname}', leave=False):
@@ -189,7 +189,7 @@ def peaks(testname, inputdir, maskdir, mask_extension):
                                '-npass', '2',
                                '-config', 'RealignTransform', 'False',
                                '-quiet'])
-        proc = subprocess.run(['peakscheck', op.join(inputdir, f'{v}.mif'),
+        proc = subprocess.run(['peakscheck', op.join(inputdir, f'{v}.{image_extension}'),
                                '-mask', maskpath,
                                '-quiet'],
                               capture_output=True)