From a4188ec326cd00eb4f951065701311ff5416d52c Mon Sep 17 00:00:00 2001
From: anroy1 <a.royer111@gmail.com>
Date: Sat, 20 Apr 2024 17:51:18 +0000
Subject: [PATCH] Swith transform format to freesurfer standard

---
 modules/nf-scil/registration/synthregistration/main.nf | 10 +++++-----
 .../nf-scil/registration/synthregistration/meta.yml    |  6 +++---
 tests/config/pytest_modules.yml                        |  5 +++++
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
index 5ceb177e5..1131c3019 100644
--- a/modules/nf-scil/registration/synthregistration/main.nf
+++ b/modules/nf-scil/registration/synthregistration/main.nf
@@ -11,7 +11,7 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     output:
     tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image
-    tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform
+    tuple val(meta), path("*__deform_warp.mgz"), emit: deform_transform
     tuple val (meta), path("*__init_warp.lta"), emit: init_transform
     path "versions.yml"           , emit: versions
 
@@ -36,8 +36,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
-    mri_synthmorph $init -g -t ${prefix}__init_warp.lta $moving $fixed
-    mri_synthmorph $warp -g -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.nii.gz -o ${prefix}__output_warped.nii.gz $moving $fixed
+    mri_synthmorph $init -t ${prefix}__init_warp.lta $moving $fixed
+    mri_synthmorph $warp $gpu $smooth $extent $weight -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.mgz -o ${prefix}__output_warped.nii.gz $moving $fixed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -53,8 +53,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     mri_synthmorph -h
 
     touch ${prefix}__output_warped.nii.gz
-    touch ${prefix}__deform_warp.nii.gz
-    touch ${prefix}__init_warp.txt
+    touch ${prefix}__deform_warp.mgz
+    touch ${prefix}__init_warp.lta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
index e4ba75452..d51d62086 100644
--- a/modules/nf-scil/registration/synthregistration/meta.yml
+++ b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -1,6 +1,6 @@
 ---
 name: "registration_synthregistration"
-description: Perform registration using SynthMorph from Freesurfer
+description: Perform registration using SynthMorph from Freesurfer. Output transforms in Freesurfer format .lta for affine and .mgz for deform, which can be converted for ANTs with respectively lta_convert and mri_warp_convert.
 keywords:
   - registration
   - Brain imaging
@@ -43,12 +43,12 @@ output:
   - init_transform:
       type: file
       description: Affine transform for initialization
-      pattern: "*.{lta}"
+      pattern: "*.{txt}"
 
   - deform_transform:
       type: file
       description: Deform transformation
-      pattern: "*.{nii,.nii.gz}"
+      pattern: "*.{mgz}"
 
   - warped_image:
       type: file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a29213b08..886db2f0a 100755
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -10,6 +10,7 @@ betcrop/fslbetcrop:
 bundle/recognize:
   - modules/nf-scil/bundle/recognize/**
   - tests/modules/nf-scil/bundle/recognize/**
+
 denoising/mppca:
   - modules/nf-scil/denoising/mppca/**
   - tests/modules/nf-scil/denoising/mppca/**
@@ -81,6 +82,10 @@ subworkflows/load_test_data:
   - subworkflows/nf-scil/load_test_data/**
   - tests/subworkflows/nf-scil/load_test_data/**
 
+testdata/scilpy:
+  - modules/nf-scil/testdata/scilpy/**
+  - tests/modules/nf-scil/testdata/scilpy/**
+
 testdata/sizeof:
   - modules/nf-scil/testdata/sizeof/**
   - tests/modules/nf-scil/testdata/sizeof/**