update dipy version, fix output_resolution arg and update dtifit outputs

Author: josephmje

dmriprep/cli.py

@@ -97,6 +97,7 @@ def __init__(
     "--output_resolution",
     help="The isotropic voxel size in mm the data will be resampled to before eddy.",
     type=float,
+    multiple=True
 )
 # specific options for eddy
 @click.option(
@@ -218,6 +219,9 @@ def main(
     if not work_dir:
         work_dir = os.path.join(output_dir, "scratch")
 
+    if len(output_resolution) == 1:
+        output_resolution = output_resolution * 3
+
     # Set parameters based on CLI, pass through object
     parameters = Parameters(
         layout=layout,
@@ -228,7 +232,7 @@ def main(
         work_dir=work_dir,
         ignore=list(ignore),
         b0_thresh=b0_thresh,
-        output_resolution=(output_resolution, output_resolution, output_resolution),
+        output_resolution=output_resolution,
         bet_dwi=bet_dwi,
         bet_mag=bet_mag,
         omp_nthreads=omp_nthreads,

dmriprep/workflows/dwi/base.py

@@ -94,6 +94,21 @@ def init_dwi_preproc_wf(subject_id, dwi_file, metadata, parameters):
     dwi_prep_wf = init_prep_dwi_wf(parameters.ignore, parameters.output_resolution)
 
     def gen_index(in_file):
+        """
+        Create an index file that tells `eddy` which line/lines in the
+        `acqparams.txt` file are relevant for the dwi data passed into `eddy`
+
+        **Inputs**
+
+        in_file
+            The bval file.
+
+        **Outputs**
+
+        out_file
+            The output index file.
+        """
+
         import os
         import numpy as np
         import nibabel as nib
@@ -393,6 +408,9 @@ def get_b0_mask_fn(b0_file):
                 outputnode,
                 [
                     ("outputnode.FA_file", "out_dtifit_FA"),
+                    ("outputnode.MD_file", "out_dtifit_MD"),
+                    ("outputnode.AD_file", "out_dtifit_AD"),
+                    ("outputnode.RD_file", "out_dtifit_RD"),
                     ("outputnode.V1_file", "out_dtifit_V1"),
                     ("outputnode.sse_file", "out_dtifit_sse"),
                 ],

dmriprep/workflows/dwi/outputs.py

@@ -24,6 +24,9 @@ def init_output_wf(subject_id, session_id, output_folder):
                 "eddy_quad_json",
                 "eddy_quad_pdf",
                 "dtifit_FA",
+                "dtifit_MD",
+                "dtifit_AD",
+                "dtifit_RD",
                 "dtifit_V1",
                 "dtifit_sse",
                 "noise",
@@ -77,6 +80,8 @@ def build_path(output_folder, subject_id, session_id):
                     ("dtifit_MD", "@result.@md"),
                     ("dtifit_AD", "@result.@ad"),
                     ("dtifit_RD", "@result.@rd"),
+                    ("dtifit_V1", "@result.@v1"),
+                    ("dtifit_sse", "@result.@sse"),
                 ],
             ),
         ]

dmriprep/workflows/dwi/tensor.py

@@ -17,7 +17,7 @@ def init_tensor_wf():
 
     outputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["FA_file", "MD_file", "AD_file", "RD_file", "sse_file", "V1_file"]
+            fields=["FA_file", "MD_file", "AD_file", "RD_file", "V1_file", "sse_file"]
         ),
         name="outputnode",
     )
@@ -50,8 +50,8 @@ def init_tensor_wf():
                     ("FA", "FA_file"),
                     ("MD", "MD_file"),
                     ("L1", "AD_file"),
-                    ("sse", "sse_file"),
                     ("V1", "V1_file"),
+                    ("sse", "sse_file"),
                 ],
             ),
         ]

requirements.txt

@@ -1,10 +1,10 @@
 Click>=7.0
-dipy==0.16.0
+dipy==1.0.0
 duecredit==0.7.0
 nipype==1.2.0
 pandas==0.25.0
 parse==1.12.0
-tqdm==4.32.2
-pybids==0.9.2
+tqdm==4.33.0
+pybids==0.9.3
 matplotlib==3.1.1
-numba==0.45.0
+numba==0.45.1

setup.cfg

@@ -63,7 +63,6 @@ docs =
     %(doc)s
 duecredit = duecredit
 resmon =
-sentry = sentry-sdk >=0.6.9
 tests =
     coverage
     codecov
@@ -72,7 +71,6 @@ all =
     %(datalad)s
     %(doc)s
     %(duecredit)s
-    %(sentry)s
     %(tests)s
 
 [options.package_data]