remove env7 and split rules reg_t2_to_t1/ref into 2 rules respectively

khanlab · Jan 21, 2025 · b661b82 · b661b82
1 parent 4842076
commit b661b82
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Showing 2 changed files with 65 additions and 31 deletions.
diff --git a/hippunfold/workflow/envs/env7.yaml b/hippunfold/workflow/envs/env7.yaml
diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk
@@ -78,7 +78,7 @@ def get_floating_n4_t2(wildcards):
     return t2_imgs[int(wildcards.idx)]
 
 
-rule reg_t2_to_ref:
+rule reg_t2_to_ref_part1:
     input:
         ref=get_ref_n4_t2,
         flo=get_floating_n4_t2,
@@ -93,33 +93,55 @@ rule reg_t2_to_ref:
             desc="rigid",
             type_="ras"
         ),
-        xfm_itk=bids(
+        warped=bids(
+            root=work,
+            datatype="anat",
+            suffix="T2w.nii.gz",
+            desc="aligned",
+            floating="{idx}",
+            **inputs.subj_wildcards,
+        ),
+    container:
+        config["singularity"]["autotop"]
+    conda:
+        "../envs/niftyreg.yaml"
+    group:
+        "subj"
+    shell:
+        "reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac"
+
+rule reg_t2_to_ref_part2:
+    input:
+        xfm_ras=bids(
             root=work,
             datatype="warps",
             **inputs.subj_wildcards,
             suffix="xfm.txt",
             from_="T2w{idx}",
             to="T2w0",
             desc="rigid",
-            type_="itk"
+            type_="ras"
         ),
-        warped=bids(
+    output:
+        xfm_itk=bids(
             root=work,
-            datatype="anat",
-            suffix="T2w.nii.gz",
-            desc="aligned",
-            floating="{idx}",
+            datatype="warps",
             **inputs.subj_wildcards,
+            suffix="xfm.txt",
+            from_="T2w{idx}",
+            to="T2w0",
+            desc="rigid",
+            type_="itk"
         ),
     container:
         config["singularity"]["autotop"]
     conda:
-        "../envs/env7.yaml"
+        "../envs/c3d.yaml"
     group:
         "subj"
     shell:
-        "reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac && "
-        "c3d_affine_tool  {output.xfm_ras} -oitk {output.xfm_itk}"
+        "c3d_affine_tool  {input.xfm_ras} -oitk {output.xfm_itk}"
+
 
 
 def get_aligned_n4_t2(wildcards):
@@ -191,7 +213,7 @@ else:
             "{params.cmd}"
 
 
-rule reg_t2_to_t1:
+rule reg_t2_to_t1_part1:
     input:
         flo=bids(
             root=root,
@@ -226,35 +248,56 @@ rule reg_t2_to_t1:
             desc="rigid",
             type_="ras"
         ),
-        xfm_itk=bids(
+    log:
+        bids(
+            root="logs",
+            **inputs.subj_wildcards,
+            suffix="reg.txt",
+            from_="T2w",
+            to="T1w",
+            desc="rigid",
+            type_="ras"
+        ),
+    container:
+        config["singularity"]["autotop"]
+    conda:
+        "../envs/niftyreg.yaml"
+    group:
+        "subj"
+    shell:
+        "reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac &> {log}"
+
+rule reg_t2_to_t1_part2:
+    input:
+        xfm_ras=bids(
             root=work,
             datatype="warps",
             **inputs.subj_wildcards,
             suffix="xfm.txt",
             from_="T2w",
             to="T1w",
             desc="rigid",
-            type_="itk"
+            type_="ras"
         ),
-    log:
-        bids(
-            root="logs",
+    output:
+        xfm_itk=bids(
+            root=work,
+            datatype="warps",
             **inputs.subj_wildcards,
-            suffix="reg.txt",
+            suffix="xfm.txt",
             from_="T2w",
             to="T1w",
             desc="rigid",
-            type_="ras"
+            type_="itk"
         ),
     container:
         config["singularity"]["autotop"]
     conda:
-        "../envs/env7.yaml"
+        "../envs/c3d.yaml"
     group:
         "subj"
     shell:
-        "reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac &> {log} && "
-        "c3d_affine_tool  {output.xfm_ras} -oitk {output.xfm_itk}"
+        "c3d_affine_tool {input.xfm_ras} -oitk {output.xfm_itk}"
 
 
 def get_inputs_compose_t2_xfm_corobl(wildcards):