From 1b701f47eeb41405394362180af805d56c477b44 Mon Sep 17 00:00:00 2001
From: Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
Date: Fri, 9 Feb 2024 09:09:55 +0000
Subject: [PATCH] Added info for how to fix sMRI files.

---
 examples/fix_smri_files.py      | 29 +++++++++++++++++++++++++++++
 osl/source_recon/rhino/utils.py | 10 ++++++++--
 2 files changed, 37 insertions(+), 2 deletions(-)
 create mode 100644 examples/fix_smri_files.py

diff --git a/examples/fix_smri_files.py b/examples/fix_smri_files.py
new file mode 100644
index 00000000..59cb2c0e
--- /dev/null
+++ b/examples/fix_smri_files.py
@@ -0,0 +1,29 @@
+"""Fix sform code of structurals.
+
+This script uses FSL to set the sform code of any structural
+whose sform code is not 1 or 4 to make sure it is compatible
+with OSL.
+
+Warning: this script will permanently change the SMRI file.
+"""
+
+import nibabel as nib
+
+from osl import source_recon
+
+source_recon.setup_fsl("/path/to/fsl")
+
+# Paths to files to fix
+files = [
+    "smri/sub-001.nii.gz",
+    "smri/sub-002.nii.gz",
+]
+
+for file in files:
+    smri = nib.load(file)
+    sformcode = smri.header.get_sform(coded=True)[-1]
+    if sformcode not in [1, 4]:
+        cmd = f"fslorient -setsformcode 1 {file}"
+        source_recon.rhino.utils.system_call(cmd)
+
+print("Done”)
diff --git a/osl/source_recon/rhino/utils.py b/osl/source_recon/rhino/utils.py
index 01ec13bb..ee6f53c7 100644
--- a/osl/source_recon/rhino/utils.py
+++ b/osl/source_recon/rhino/utils.py
@@ -281,7 +281,10 @@ def _get_sform(nii_file):
     if sformcode == 1 or sformcode == 4:
         sform = nib.load(nii_file).header.get_sform()
     else:
-        raise ValueError("sform code for {} is {}, and needs to be 4 or 1".format(nii_file, sformcode))
+        raise ValueError(
+            f"sform code for {nii_file} is {sformcode}, and needs to be 4 or 1.\n"
+            "To fix see: https://github.com/OHBA-analysis/osl/blob/main/examples/fix_smri_files.py"
+        )
 
     sform = Transform("mri_voxel", "mri", sform)
     return sform
@@ -299,7 +302,10 @@ def _get_mni_sform(nii_file):
     if sformcode == 1 or sformcode == 4:
         sform = nib.load(nii_file).header.get_sform()
     else:
-        raise ValueError("sform code for {} is {}, and needs to be 4 or 1".format(nii_file, sformcode))
+        raise ValueError(
+            f"sform code for {nii_file} is {sformcode}, and needs to be 4 or 1.\n"
+            "To fix see: https://github.com/OHBA-analysis/osl/blob/main/examples/fix_smri_files.py"
+        )
 
     sform = Transform("unknown", "mni_tal", sform)
     return sform