From 67dae66c75810ecbd8b69fe73a59f39f2faf6e43 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Tue, 7 May 2024 12:19:44 +0200
Subject: [PATCH] Adding new wrapper to bedpostx
---
fsl/wrappers/__init__.py | 1 +
fsl/wrappers/bedpostx.py | 21 +++++++++++++++++++++
2 files changed, 22 insertions(+)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 6cba0e026..bed50b264 100755
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -166,6 +166,7 @@ from fsl.wrappers.bedpostx import (xfibres,
xfibres_gpu,
split_parts_gpu,
bedpostx_postproc_gpu,
+ bedpostx_postproc,
probtrackx,
probtrackx2,
probtrackx2_gpu)
diff --git a/fsl/wrappers/bedpostx.py b/fsl/wrappers/bedpostx.py
index d9a9b7e2f..18fbccdbc 100644
--- a/fsl/wrappers/bedpostx.py
+++ b/fsl/wrappers/bedpostx.py
@@ -160,6 +160,27 @@ def bedpostx_postproc_gpu(data, mask, bvecs, bvals, TotalNumVoxels,
return cmd
+@wutils.fileOrImage('data', 'mask',)
+@wutils.fileOrArray('bvecs', 'bvals')
+@wutils.fslwrapper
+def bedpostx_postproc(data, mask, bvecs, bvals, TotalNumVoxels,
+ TotalNumParts, SubjectDir, bindir, **kwargs):
+ """Wrapper for the ``bedpostx_postproc`` command."""
+
+ asrt.assertFileExists(data, bvecs, bvals)
+ asrt.assertIsNifti(mask)
+
+ cmd = ['bedpostx_postproc.sh',
+ '--data=' + data,
+ '--mask=' + mask,
+ '--bvecs=' + bvecs,
+ '--bvals=' + bvals]
+
+ cmd += wutils.applyArgStyle('--=', valmap=XFIBRES_VALMAP, **kwargs)
+ cmd += [str(TotalNumVoxels), str(TotalNumParts), SubjectDir, bindir]
+ return cmd
+
+
@wutils.fileOrImage('mask', 'seed')
@wutils.fslwrapper
def probtrackx(samples, mask, seed, **kwargs):
--
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