Making the diffusion more flexible

bip/pipelines/dMRI_diff/diff_autoptx.py

@@ -47,8 +47,9 @@ def run(ctx,
                           outdir=logs_dir):
 
         t_name  = autoptx_tract.value
-        # TODO: Allow for customization for this multiplication factor
-        t_seeds = int(ctx.tract_struct[t_name]["num_seeds"] * 300)
+
+        seed_mult = ctx.get('dMRI_multiplier_autoPtx_seeds', 300)
+        t_seeds = int(ctx.tract_struct[t_name]["num_seeds"] * seed_mult)
 
         orig_tract_dir = ctx.get_data('dMRI/autoptx/protocols/' + t_name + '/')
         FMRIB58_FA_1mm = ctx.get_standard('FMRIB58_FA_1mm.nii.gz')

bip/pipelines/dMRI_diff/diff_dtifit.py

@@ -37,12 +37,11 @@ def run(ctx,
         list_vals = []
         b_vals = np.loadtxt(eddy_bvals)
         b_vecs = np.loadtxt(eddy_bvecs)
-        lim_file = ctx.get_data('dMRI/b0_threshold.txt')
+        lim_file = ctx.get('dMRI_b0_threshold', 100)
 
         lim = int(np.loadtxt(lim_file))
 
-        # TODO: This can be modifiable by the user
-        b_value_shell_to_keep = 1000
+        b_value_shell_to_keep = ctx.get('dMRI_b_value_shell', 1000)
 
         for count, b_val in enumerate(b_vals):
             # These are the b0 images: They are automatically included

bip/pipelines/dMRI_diff/diff_eddy.py

@@ -7,7 +7,7 @@
 # Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
 #
 # pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
-# pylint: disable=W0613
+# pylint: disable=W0613,W0719,R0912
 #
 
 import os
@@ -23,8 +23,10 @@ log = logging.getLogger(__name__)
 
 def run(ctx,
         AP:                             In,
-        AP_bval:                        In,
-        AP_bvec:                        In,
+        AP_bval:                        In(optional=True),
+        AP_bvec:                        In(optional=True),
+        PA_bval:                        In(optional=True),
+        PA_bvec:                        In(optional=True),
         AP_best_index:                  In,
         fieldmap_iout_mean:             In,
         fieldmap_mask:                  In,
@@ -45,6 +47,32 @@ def run(ctx,
 
     with redirect_logging(job_name(run), outdir=logs_dir):
 
+        # Adapting the code to let the user use commin BVAL and BVEC files
+        folder_b_files = ctx.get("dMRI_b_files", "")
+
+        if op.exists(folder_b_files):
+            new_AP_bval = op.join(folder_b_files, "AP.bval")
+            new_PA_bval = op.join(folder_b_files, "PA.bval")
+            new_AP_bvec = op.join(folder_b_files, "AP.bvec")
+            new_PA_bvec = op.join(folder_b_files, "PA.bvec")
+
+            if op.exists(new_AP_bval):
+                copyfile(src=new_AP_bval, dst=AP_bval)
+            else:
+                raise Exception("Missing AP.bval in " + folder_b_files)
+            if op.exists(new_PA_bval):
+                copyfile(src=new_PA_bval, dst=PA_bval)
+            else:
+                raise Exception("Missing PA.bval in " + folder_b_files)
+            if op.exists(new_AP_bvec):
+                copyfile(src=new_AP_bvec, dst=AP_bvec)
+            else:
+                raise Exception("Missing AP.bvec in " + folder_b_files)
+            if op.exists(new_PA_bvec):
+                copyfile(src=new_PA_bvec, dst=PA_bvec)
+            else:
+                raise Exception("Missing PA.bvec in " + folder_b_files)
+
         # Creates links
         if eddy_AP is not None and not op.exists(eddy_AP):
             rel_path = op.relpath(AP, op.dirname(eddy_AP))

bip/pipelines/dMRI_diff/diff_tbss.py

@@ -133,8 +133,7 @@ def run(ctx,
             run(TBSS_mean_FA_skeleton)
 
         # Create Skeleton mask
-        # TODO: This threshold could be configurable by user
-        thresh = 2000
+        thresh = ctx.get('dMRI_TBSS_skeleton_threshold', 2000)
         wrappers.fslmaths(TBSS_mean_FA_skeleton).thr(thresh).bin().\
             run(TBSS_mean_FA_skeleton_mask)
         wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_skeleton_mask).\