From ba785f11c7e8b721015305da42988af9d8a88835 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Fri, 10 Jan 2025 16:41:24 -0500
Subject: [PATCH] WIP: laynii for equivolume/equidistant coords

tried it out and works great! this is a placeholder for me to complete
later..
---
 hippunfold/workflow/rules/autotop.smk | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk
index 22e1d4f3..f482fb34 100644
--- a/hippunfold/workflow/rules/autotop.smk
+++ b/hippunfold/workflow/rules/autotop.smk
@@ -221,3 +221,15 @@ rule equivolume_coords:
         config["singularity"]["autotop"]
     shell:
         "python {params.script} {resources.tmpdir} {input.innerbin} {input.outerbin} {output.coords} &> {log}"
+
+"""
+rule prep_dseg_for_laynii:
+    input
+    shell:
+        "c3d ../hippunfold_khanlab/test_wbdev/test_wbdev/work/sub-1425/anat/sub-1425_hemi-L_space-corobl_desc-postproc_dseg.nii.gz -as DSEG -retain-labels 1 8 -binarize -scale 3 -popas GM -push DSEG -retain-labels 2 4 7 -binarize -scale 2 -popas WM -push DSEG -replace 0 100 -retain-labels  100 -binarize -scale 1 -popas PIAL -push GM -push WM -add -push PIAL -add -o sub-1425_hemi-L_desc-rim_dseg.nii.gz"
+
+rule laynii_layers:
+    input:
+    shell:
+        "LN2_LAYERS  -rim sub-1425_hemi-L_desc-rim_dseg.nii.gz  -equivol"
+"""