SynthSR+SyN for fieldmap-less distortion correction (#50)

This implements a novel SynthSR+SyN method for fieldmap-less distortion correction. It is similar to the SyN method used in SDCFlows, except, the b0 and T1w images are transformed to T1w-like 1mm images before performing registration, which makes the registration much more robust.

This is now set-up as a the default method to use when topup cannot be used (ie no opposite phase encoding directions).

Also a couple other miscellaneous changes here:

-add shadow to synthstrip/synthsr rules
-disable bedpost by default

snakedwi/config/snakebids.yml

@@ -13,11 +13,6 @@ derivatives: False
 analysis_levels: &analysis_levels
  - participant
 
-no_topup: False
-use_eddy_s2v: False
-eddy_no_quad: False
-no_bedpost: False
-use_syn_sdc: False
 
 targets_by_analysis_level:
   participant:
@@ -92,10 +87,16 @@ parse_args:
     action: 'store_true'
     default: False
 
-  --no_bedpost:
-    help: 'Disable bedpost  (default: %(default)s)'
-    action: 'store_true'
-    default: False
+  --use_bedpost: 
+    help: 'Enable bedpost  (disabled by default)'
+    action: 'store_false'
+    dest: 'no_bedpost'
+    default: True
+
+    #  --no_bedpost:
+    #    help: 'Disable bedpost  (default: %(default)s)'
+    #    action: 'store_true'
+    #    default: True
 
 
   --use_eddy_s2v:
@@ -156,6 +157,16 @@ parse_args:
     action: 'store_true'
     default: False
 
+    #  --synthsr_sdc:
+    #help: "Enable SynthSR+SyN fieldmap-less distortion-correction. This uses SynthSR to transform T1w and b0 images to the same 1mm T1w contrast prior to non-linear registration to obtain a field-map. (default: %(default)s)"
+    #action: 'store_true'
+    #default: True
+
+  --no_synthsr_sdc:
+    help: "Disable SynthSR+SyN fieldmap-less distortion-correction (enabled by default)"
+    action: 'store_false'
+    dest: 'use_synthsr_sdc'
+    default: True
 
 
 #---- to update below this
@@ -173,6 +184,9 @@ singularity:
   python: 'docker://khanlab/pythondeps-snakedwi:v0.2.0'  
   synthstrip: 'docker://freesurfer/synthstrip:1.3'
   sdcflows: 'docker://nipreps/fmriprep:22.1.1' #can't currently just use sdcflows docker as it is missing freesurfer's mri_robust_template
+  synthsr: 'docker://akhanf/synthsr:main'
+  synthmorph: 'docker://freesurfer/synthmorph:1'
+
 
 
 
@@ -281,6 +295,7 @@ eddy:
 default_effective_echo_spacing: 0.0001 #if not defined in JSON files
 
 #for test data
+root: 'results'
 participant_label: 
 exclude_participant_label:
 masking_method: b0_synthstrip
@@ -292,4 +307,7 @@ use_eddy_gpu: False
 use_bedpost_gpu: False
 rigid_dwi_t1_init: 'identity'
 rigid_dwi_t1_iters: '50x50'
-root: 'results'
+eddy_no_quad: False
+no_topup: False
+use_syn_sdc: False
+use_synthsr_sdc: True 

snakedwi/workflow/rules/eddy.smk

@@ -101,6 +101,17 @@ def get_eddy_topup_fmap_input(wildcards):
                 **subj_wildcards,
             ).format(**wildcards),
         }
+    elif method == "synthsr":
+        return {
+            "fmap": bids(
+                root=work,
+                datatype="dwi",
+                suffix="fmap.nii.gz",
+                desc="b0",
+                method="synthSRsdc",
+                **subj_wildcards,
+            ).format(**wildcards)
+        }
     elif method == "syn":
         return {
             "fmap": bids(
@@ -130,6 +141,17 @@ def get_eddy_topup_fmap_opt(wildcards, input):
             root=work, suffix="topup", datatype="dwi", **subj_wildcards
         ).format(**wildcards)
         return f"--topup={topup_prefix}"
+    elif method == "synthsr":
+        fmap_prefix = bids(
+            root=work,
+            datatype="dwi",
+            suffix="fmap",
+            desc="b0",
+            method="synthSRsdc",
+            **subj_wildcards,
+        ).format(**wildcards)
+        return f"--field={fmap_prefix}"
+
     elif method == "syn":
         fmap_prefix = bids(
             root=work,

snakedwi/workflow/rules/masking_b0_synthstrip.smk

@@ -22,6 +22,8 @@ rule synthstrip_b0:
     container:
         config["singularity"]["synthstrip"]
     threads: 8
+    shadow:
+        "minimal"
     group:
         "subj"
     shell:

snakedwi/workflow/rules/reg_dwi_to_t1.smk

@@ -30,6 +30,8 @@ rule synthstrip_t1:
     container:
         config["singularity"]["synthstrip"]
     threads: 8
+    shadow:
+        "minimal"
     shell:
         "python3 /freesurfer/mri_synthstrip -i {input.t1} -m {output.mask}"
 

snakedwi/workflow/rules/reg_t1_to_template.smk

@@ -54,8 +54,8 @@ rule convert_template_xfm_ras2itk:
             datatype="transforms",
             **subj_wildcards,
             suffix="xfm.txt",
-            from_="subject",
-            to="{template}",
+            from_="{from}",
+            to="{to}",
             desc="{desc}",
             type_="ras"
         ),
@@ -65,8 +65,8 @@ rule convert_template_xfm_ras2itk:
             datatype="transforms",
             **subj_wildcards,
             suffix="xfm.txt",
-            from_="subject",
-            to="{template}",
+            from_="{from}",
+            to="{to}",
             desc="{desc}",
             type_="itk"
         ),