-stride --> -strides

bin/dwi2response

@@ -81,9 +81,9 @@ app.makeTempDir()
 
 # Get standard input data into the temporary directory
 if alg.needsSingleShell() or shells_option:
-  run.command('mrconvert ' + path.fromUser(app.args.input, True) + ' - -stride 0,0,0,1' + grad_import_option + ' | dwiextract - ' + path.toTemp('dwi.mif', True) + shells_option + singleshell_option)
+  run.command('mrconvert ' + path.fromUser(app.args.input, True) + ' - -strides 0,0,0,1' + grad_import_option + ' | dwiextract - ' + path.toTemp('dwi.mif', True) + shells_option + singleshell_option)
 else: # Don't discard b=0 in multi-shell algorithms
-  run.command('mrconvert ' + path.fromUser(app.args.input, True) + ' ' + path.toTemp('dwi.mif', True) + ' -stride 0,0,0,1' + grad_import_option)
+  run.command('mrconvert ' + path.fromUser(app.args.input, True) + ' ' + path.toTemp('dwi.mif', True) + ' -strides 0,0,0,1' + grad_import_option)
 if app.args.mask:
   run.command('mrconvert ' + path.fromUser(app.args.mask, True) + ' ' + path.toTemp('mask.mif', True) + ' -datatype bit')
 else:

bin/dwibiascorrect

@@ -91,7 +91,7 @@ run.command('dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3')
 if app.args.fsl:
 
   # FAST doesn't accept a mask input; therefore need to explicitly mask the input image
-  run.command('mrcalc mean_bzero.mif mask.mif -mult - | mrconvert - mean_bzero_masked.nii -stride -1,+2,+3')
+  run.command('mrcalc mean_bzero.mif mask.mif -mult - | mrconvert - mean_bzero_masked.nii -strides -1,+2,+3')
   run.command(fast_cmd + ' -t 2 -o fast -n 3 -b mean_bzero_masked.nii')
   bias_path = fsl.findImage('fast_bias')
 
@@ -105,8 +105,8 @@ elif app.args.ants:
 
   # Use the brain mask as a weights image rather than a mask; means that voxels at the edge of the mask
   #   will have a smoothly-varying bias field correction applied, rather than multiplying by 1.0 outside the mask
-  run.command('mrconvert mean_bzero.mif mean_bzero.nii -stride +1,+2,+3')
-  run.command('mrconvert mask.mif mask.nii -stride +1,+2,+3')
+  run.command('mrconvert mean_bzero.mif mean_bzero.nii -strides +1,+2,+3')
+  run.command('mrconvert mask.mif mask.nii -strides +1,+2,+3')
   bias_path = 'bias.nii'
   run.command('N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,' + bias_path + '] -s 4 -b [100,3] -c [1000,0.0]')
 

bin/dwigradcheck

@@ -43,7 +43,7 @@ num_volumes = image_dimensions[3]
 app.makeTempDir()
 
 # Make sure the image data can be memory-mapped
-run.command('mrconvert ' + app.args.input + ' ' + path.toTemp('data.mif', True) + ' -stride 0,0,0,1 -datatype float32')
+run.command('mrconvert ' + app.args.input + ' ' + path.toTemp('data.mif', True) + ' -strides 0,0,0,1 -datatype float32')
 
 if app.args.grad:
   shutil.copy(path.fromUser(app.args.grad, False), path.toTemp('grad.b', False))

bin/dwipreproc

@@ -733,7 +733,7 @@ if do_topup:
 
 
   # Do the conversion in preparation for topup
-  run.command('mrconvert ' + se_epi_path + ' topup_in.nii' + import_se_epi_manual_pe_table_option + ' -stride -1,+2,+3,+4 -export_pe_table topup_datain.txt')
+  run.command('mrconvert ' + se_epi_path + ' topup_in.nii' + import_se_epi_manual_pe_table_option + ' -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt')
   file.delTemporary(se_epi_path)
 
   # Run topup
@@ -788,7 +788,7 @@ if do_topup:
 else:
 
   # Generate a processing mask for eddy based on the uncorrected input DWIs
-  run.command('dwi2mask ' + dwi_path + ' - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -stride -1,+2,+3')
+  run.command('dwi2mask ' + dwi_path + ' - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3')
 
 
 # Generate the text file containing slice timing / grouping information if necessary
@@ -827,7 +827,7 @@ eddy_manual_options = (' ' + ' '.join(eddy_manual_options)) if eddy_manual_optio
 
 
 # Run eddy
-run.command('mrconvert ' + dwi_path + import_dwi_pe_table_option + dwi_permute_volumes_pre_eddy_option + ' eddy_in.nii -stride -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt')
+run.command('mrconvert ' + dwi_path + import_dwi_pe_table_option + dwi_permute_volumes_pre_eddy_option + ' eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt')
 file.delTemporary(dwi_path)
 run.command(eddy_cmd + ' --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals' + eddy_in_topup_option + eddy_manual_options + ' --out=dwi_post_eddy')
 file.delTemporary('eddy_in.nii')
@@ -838,7 +838,7 @@ eddy_output_image_path = fsl.findImage('dwi_post_eddy')
 
 
 # Get the axis strides from the input series, so the output image can be modified to match
-stride_option = ' -stride ' + ','.join([str(i) for i in dwi_header.stride()])
+stride_option = ' -strides ' + ','.join([str(i) for i in dwi_header.stride()])
 
 
 # Check to see whether or not eddy has provided a rotated bvecs file;

bin/labelsgmfix

@@ -75,9 +75,9 @@ app.makeTempDir()
 # Get the parcellation and T1 images into the temporary directory, with conversion of the T1 into the correct format for FSL
 run.command('mrconvert ' + path.fromUser(app.args.parc, True) + ' ' + path.toTemp('parc.mif', True))
 if upsample_for_first:
-  run.command('mrresize ' + path.fromUser(app.args.t1, True) + ' - -voxel 1.0 -interp sinc | mrcalc - 0.0 -max - | mrconvert - ' + path.toTemp('T1.nii', True) + ' -stride -1,+2,+3')
+  run.command('mrresize ' + path.fromUser(app.args.t1, True) + ' - -voxel 1.0 -interp sinc | mrcalc - 0.0 -max - | mrconvert - ' + path.toTemp('T1.nii', True) + ' -strides -1,+2,+3')
 else:
-  run.command('mrconvert ' + path.fromUser(app.args.t1, True) + ' ' + path.toTemp('T1.nii', True) + ' -stride -1,+2,+3')
+  run.command('mrconvert ' + path.fromUser(app.args.t1, True) + ' ' + path.toTemp('T1.nii', True) + ' -strides -1,+2,+3')
 
 app.gotoTempDir()
 

cmd/mrinfo.cpp

@@ -76,7 +76,7 @@ void usage ()
     +   Option ("size", "image size along each axis")
     +   Option ("spacing", "voxel spacing along each image dimension")
     +   Option ("datatype", "data type used for image data storage")
-    +   Option ("stride", "data strides i.e. order and direction of axes data layout")
+    +   Option ("strides", "data strides i.e. order and direction of axes data layout")
     +   Option ("offset", "image intensity offset")
     +   Option ("multiplier", "image intensity multiplier")
     +   Option ("transform", "the voxel to image transformation")
@@ -236,7 +236,7 @@ void header2json (const Header& header, nlohmann::json& json)
   json["spacing"] = spacing;
   vector<ssize_t> strides (Stride::get (header));
   Stride::symbolise (strides);
-  json["stride"] = strides;
+  json["strides"] = strides;
   json["format"] = header.format();
   json["datatype"] = header.datatype().specifier();
   json["intensity_offset"] = header.intensity_offset();
@@ -278,7 +278,7 @@ void run ()
   const bool size        = get_options("size")          .size();
   const bool spacing     = get_options("spacing")       .size();
   const bool datatype    = get_options("datatype")      .size();
-  const bool stride      = get_options("stride")        .size();
+  const bool strides     = get_options("strides")       .size();
   const bool offset      = get_options("offset")        .size();
   const bool multiplier  = get_options("multiplier")    .size();
   const auto properties  = get_options("property");
@@ -289,7 +289,7 @@ void run ()
   const bool raw_dwgrad  = get_options("raw_dwgrad")    .size();
   const bool petable     = get_options("petable")       .size();
 
-  const bool print_full_header = !(format || ndim || size || spacing || datatype || stride ||
+  const bool print_full_header = !(format || ndim || size || spacing || datatype || strides ||
       offset || multiplier || properties.size() || transform ||
       dwgrad || export_grad || shellvalues || shellcounts || export_pe || petable ||
       json_keyval || json_all);
@@ -306,7 +306,7 @@ void run ()
     if (size)       print_dimensions (header);
     if (spacing)    print_spacing (header);
     if (datatype)   std::cout << (header.datatype().specifier() ? header.datatype().specifier() : "invalid") << "\n";
-    if (stride)     print_strides (header);
+    if (strides)    print_strides (header);
     if (offset)     std::cout << header.intensity_offset() << "\n";
     if (multiplier) std::cout << header.intensity_scale() << "\n";
     if (transform)  print_transform (header);

core/stride.cpp

@@ -23,7 +23,7 @@ namespace MR
     using namespace App;
 
     const OptionGroup Options = OptionGroup ("Stride options")
-      + Option ("stride",
+      + Option ("strides",
           "specify the strides of the output data in memory, as a comma-separated list. "
           "The actual strides produced will depend on whether the output image "
           "format can support it.")
@@ -84,7 +84,7 @@ namespace MR
 
 
       if (strides.size() > current.size())
-        WARN ("too many axes supplied to -stride option - ignoring remaining strides");
+        WARN ("too many axes supplied to -strides option - ignoring remaining strides");
       strides.resize (current.size(), 0);
 
       for (const auto x : strides)
@@ -95,7 +95,7 @@ namespace MR
         if (!strides[1]) continue;
         for (size_t j = i+1; j < strides.size(); ++j) 
           if (std::abs (strides[i]) == std::abs (strides[j])) 
-            throw Exception ("duplicate entries provided to \"-stride\" option: " + str(opt[0][0]));
+            throw Exception ("duplicate entries provided to \"-strides\" option: " + str(opt[0][0]));
       }
 
       List prev = get_symbolic (current);

docs/getting_started/image_data.rst

@@ -284,17 +284,17 @@ for applications that need to process all values for a given voxel
 concurrently (as is often the case in diffusion MRI), by allowing the hardware
 to make better use of resources (tractography is one such example).
 
-Many *MRtrix3* commands accept the ``-stride`` option, which is used to specify
+Many *MRtrix3* commands accept the ``-strides`` option, which is used to specify
 the strides for the output image. For example, to generate a LAS (radiological)
 NIfTI image for use with FSL (along with the corresponding bvecs/bvals), you
-can use :ref:`mrconvert` along with the ``-stride -1,2,3,4`` option::
+can use :ref:`mrconvert` along with the ``-strides -1,2,3,4`` option::
 
-    $ mrconvert dwi.mif -stride -1,2,3,4 -export_grad_fsl bvecs bvals dwi.nii
+    $ mrconvert dwi.mif -strides -1,2,3,4 -export_grad_fsl bvecs bvals dwi.nii
 
 Likewise, if you need to ensure the orientation is neurological (RAS), you can
 specify strides ``1,2,3,4`` (or use the ``1:4`` shorthand). You can also specify
-other combinations if required: for example ``-stride -2,-1,3,4`` would
-correspond to a PLS coordinate system, ``-stride 2,3,4,1`` would correspond to
+other combinations if required: for example ``-strides -2,-1,3,4`` would
+correspond to a PLS coordinate system, ``-strides 2,3,4,1`` would correspond to
 volume-contiguous storage (with RAS for the spatial axes), etc. 
 
 The different formats supported by *MRtrix3* differ in the range of strides

docs/quantitative_structural_connectivity/ismrm_hcp_tutorial.rst

@@ -95,7 +95,7 @@ Diffusion image processing
    in memory for each voxel, and convert to floating-point representation
    (makes data access faster in subsequent commands):
 
-``mrconvert data.nii.gz DWI.mif -fslgrad bvecs bvals -datatype float32 -stride 0,0,0,1``
+``mrconvert data.nii.gz DWI.mif -fslgrad bvecs bvals -datatype float32 -strides 0,0,0,1``
 
 2. Generate a mean *b*\ =0 image (useful for visualisation):
 

docs/reference/commands/amp2sh.rst

@@ -55,7 +55,7 @@ DW shell selection options
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands/dwi2fod.rst

@@ -66,7 +66,7 @@ Options for the Constrained Spherical Deconvolution algorithm
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands/dwiextract.rst

@@ -56,7 +56,7 @@ Options for selecting volumes based on phase-encoding
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands/maskfilter.rst

@@ -56,7 +56,7 @@ Options for median filter
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands/mrconvert.rst

@@ -70,7 +70,7 @@ Options to modify generic header entries
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Data type options
 ^^^^^^^^^^^^^^^^^

docs/reference/commands/mrfilter.rst

@@ -73,7 +73,7 @@ Options for smooth filter
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

docs/reference/commands/mrinfo.rst

@@ -41,7 +41,7 @@ Options
 
 -  **-datatype** data type used for image data storage
 
--  **-stride** data strides i.e. order and direction of axes data layout
+-  **-strides** data strides i.e. order and direction of axes data layout
 
 -  **-offset** image intensity offset
 

docs/reference/commands/sh2amp.rst

@@ -29,7 +29,7 @@ Options
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Data type options
 ^^^^^^^^^^^^^^^^^

docs/reference/commands/shconv.rst

@@ -27,7 +27,7 @@ Options
 Stride options
 ^^^^^^^^^^^^^^
 
--  **-stride spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
+-  **-strides spec** specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
 
 Standard options
 ^^^^^^^^^^^^^^^^

lib/mrtrix3/_5ttgen/fsl.py

@@ -24,11 +24,11 @@ def getInputs(): #pylint: disable=unused-variable
   image.check3DNonunity(path.fromUser(app.args.input, False))
   run.command('mrconvert ' + path.fromUser(app.args.input, True) + ' ' + path.toTemp('input.mif', True))
   if app.args.mask:
-    run.command('mrconvert ' + path.fromUser(app.args.mask, True) + ' ' + path.toTemp('mask.mif', True) + ' -datatype bit -stride -1,+2,+3')
+    run.command('mrconvert ' + path.fromUser(app.args.mask, True) + ' ' + path.toTemp('mask.mif', True) + ' -datatype bit -strides -1,+2,+3')
   if app.args.t2:
     if not image.match(app.args.input, app.args.t2):
       app.error('Provided T2 image does not match input T1 image')
-    run.command('mrconvert ' + path.fromUser(app.args.t2, True) + ' ' + path.toTemp('T2.nii', True) + ' -stride -1,+2,+3')
+    run.command('mrconvert ' + path.fromUser(app.args.t2, True) + ' ' + path.toTemp('T2.nii', True) + ' -strides -1,+2,+3')
 
 
 
@@ -68,7 +68,7 @@ def execute(): #pylint: disable=unused-variable
              'retaining the original higher resolution of the T1 image is preferable')
     upsample_for_first = True
 
-  run.command('mrconvert input.mif T1.nii -stride -1,+2,+3')
+  run.command('mrconvert input.mif T1.nii -strides -1,+2,+3')
 
   fast_t1_input = 'T1.nii'
   fast_t2_input = ''
@@ -206,7 +206,7 @@ def execute(): #pylint: disable=unused-variable
   run.command('mrcalc ' + fast_gm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif')
   run.command('mrcalc ' + fast_wm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif')
   run.command('mrcalc 0 wm.mif -min path.mif')
-  run.command('mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -stride +2,+3,+4,+1')
+  run.command('mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -strides +2,+3,+4,+1')
 
   # Use mrcrop to reduce file size (improves caching of image data during tracking)
   if app.args.nocrop:

lib/mrtrix3/dwi2response/manual.py

@@ -23,7 +23,7 @@ def getInputs(): #pylint: disable=unused-variable
     os.remove(mask_path)
   run.command('mrconvert ' + path.fromUser(app.args.in_voxels, True) + ' ' + path.toTemp('in_voxels.mif', True))
   if app.args.dirs:
-    run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -stride 0,0,0,1')
+    run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -strides 0,0,0,1')
 
 
 

lib/mrtrix3/dwi2response/msmt_5tt.py

@@ -26,7 +26,7 @@ def getInputs(): #pylint: disable=unused-variable
   from mrtrix3 import app, path, run
   run.command('mrconvert ' + path.fromUser(app.args.in_5tt, True) + ' ' + path.toTemp('5tt.mif', True))
   if app.args.dirs:
-    run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -stride 0,0,0,1')
+    run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -strides 0,0,0,1')
 
 
 

lib/mrtrix3/image.py

@@ -27,7 +27,7 @@ def __init__(self, image_path):
       self._name = data['name']
       self._size = data['size']
       self._spacing = data['spacing']
-      self._stride = data['stride']
+      self._strides = data['strides']
       self._format = data['format']
       self._datatype = data['datatype']
       self._intensity_offset = data['intensity_offset']
@@ -47,8 +47,8 @@ def size(self):
     return self._size
   def spacing(self):
     return self._spacing
-  def stride(self):
-    return self._stride
+  def strides(self):
+    return self._strides
   def format(self):
     return self._format
   def datatype(self):