add eddy_quad after running eddy

designer2/designer.py

@@ -95,7 +95,7 @@ def usage(cmdline): #pylint: disable=unused-variable
     rpe_options.add_argument('-rpe_all', metavar=('<reverse PE dwi volume>'), help='Specify that ALL DWIs have been acquired with opposing phase-encoding; this information will be used to perform a recombination of image volumes (each pair of volumes with the same b-vector but different phase encoding directions will be combined together into a single volume). The argument to this option is the set of volumes with reverse phase encoding but the same b-vectors as the input image')
     rpe_options.add_argument('-rpe_header', action='store_true', help='Specify that the phase-encoding information can be found in the image header(s), and that this is the information that the script should use')
     rpe_options.add_argument('-rpe_te', metavar=('<echo time (s)>'), help='Specify the echo time of the reverse phase encoded image, if it is not accompanied by a bids .json sidecar.')
-
+    rpe_options.add_argument('-eddy_quad_output', metavar=('<path>'), help='path to a not yet existing directory you want to save eddy_quad output to')
 
 def execute(): #pylint: disable=unused-variable
     from mrtrix3 import app, fsl, run, path #pylint: disable=no-name-in-module, import-outside-toplevel

docs/docs/designer/usage.md

@@ -170,6 +170,15 @@ Olesen, J. L., Ianus, A., Østergaard, L., Shemesh, N., & Jespersen, S. N. (2023
 - Perform rigid motion correction using ANTs (useful for cases where eddy breaks down).
 - Runs volume-to-volume registration for each DWI image using a mutual information cost function and b-spline interpolation.
 
+### `-eddy_quad_output <path/to/eddy_quad/output/folder>`
+- eddy_quad (QC report) will run after -eddy
+- Path to a not yet existing folder you want to save eddy_quad output to.
+- By default, it will save to the scratch (use `-nocleanup` to save scratch directory) directory (path/to/scratch/eddy_processing/dwi_post_eddy.qc)
+
+{: .ref }
+> Matteo Bastiani, Michiel Cottaar, Sean P. Fitzgibbon, Sana Suri, Fidel Alfaro-Almagro, Stamatios N.
+Sotiropoulos, Saad Joabdi and Jesper L.R. Andersson. (2019). Automated quality control for within and between studies diffusion MRI data using a non-parametric framework for movement and distortion correction. Neurolmage 184:801-812.
+
 ---
 
 ## Options relating to Gibbs artifact correction

lib/designer_func_wrappers.py

@@ -903,6 +903,25 @@ def run_eddy(shell_table, dwi_metadata):
 
         elif not app.ARGS.rpe_header and not app.ARGS.rpe_all and not app.ARGS.rpe_pair:
             raise MRtrixError("the eddy option must run alongside -rpe_header, -rpe_all, or -rpe_pair option")
+    if app.ARGS.eddy_quad_output:
+        run.command('eddy_quad "%s" -idx "%s" -par "%s" -m "%s" -b "%s" -g "%s" -o "%s"' %
+                    ('eddy_processing/dwi_post_eddy',
+                    'eddy_processing/eddy_indices.txt',
+                    'eddy_processing/eddy_config.txt',
+                    'eddy_processing/eddy_mask.nii',
+                    'eddy_processing/bvals',
+                    'eddy_processing/bvecs',
+                    app.ARGS.eddy_quad_output
+                    ))
+    else:
+        run.command('eddy_quad "%s" -idx "%s" -par "%s" -m "%s" -b "%s" -g "%s"' %
+                    ('eddy_processing/dwi_post_eddy',
+                    'eddy_processing/eddy_indices.txt',
+                    'eddy_processing/eddy_config.txt',
+                    'eddy_processing/eddy_mask.nii',
+                    'eddy_processing/bvals',
+                    'eddy_processing/bvecs'
+                    ))
 
     run.command('mrconvert -force -fslgrad working.bvec working.bval dwiec.mif working.mif', show=False)
     # End timer