From 48aaf997e1183fa830480b9aa1a2ceb87c56b4b9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 24 Mar 2020 18:23:14 +0000
Subject: [PATCH] RF: header example
---
advanced_topics/08_fslpy.ipynb | 29 ++++++++++++++++++++++++-----
advanced_topics/08_fslpy.md | 21 ++++++++++++++++-----
2 files changed, 40 insertions(+), 10 deletions(-)
diff --git a/advanced_topics/08_fslpy.ipynb b/advanced_topics/08_fslpy.ipynb
index dc39b28..acda784 100644
--- a/advanced_topics/08_fslpy.ipynb
+++ b/advanced_topics/08_fslpy.ipynb
@@ -223,8 +223,8 @@
"# load a FSL image - the file\n",
"# suffix is optional, just like\n",
"# in real FSL-land!\n",
- "img = Image(op.join(stddir, 'MNI152_T1_1mm'))\n",
- "print(img)"
+ "std1mm = Image(op.join(stddir, 'MNI152_T1_1mm'))\n",
+ "print(std1mm)"
]
},
{
@@ -243,7 +243,7 @@
"# load a nibabel image, and\n",
"# convert it into an FSL image\n",
"nibimg = nib.load(op.join(stddir, 'MNI152_T1_1mm.nii.gz'))\n",
- "img = Image(nibimg)"
+ "std1mm = Image(nibimg)"
]
},
{
@@ -259,10 +259,28 @@
"metadata": {},
"outputs": [],
"source": [
- "data = np.zeros((100, 100, 100))\n",
+ "data = np.zeros((182, 218, 182))\n",
"img = Image(data, xform=np.eye(4))"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "If you have generated some data from another `Image` (or from a\n",
+ "`nibabel.Nifti1Image`) you can use the `header` option to set\n",
+ "the header information on the new image:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "img = Image(data, header=std1mm.header)"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -276,7 +294,8 @@
"metadata": {},
"outputs": [],
"source": [
- "img.save('empty.nii.gz')"
+ "img.save('empty')\n",
+ "!ls"
]
},
{
diff --git a/advanced_topics/08_fslpy.md b/advanced_topics/08_fslpy.md
index 9cfe1d6..b8fb3b2 100644
--- a/advanced_topics/08_fslpy.md
+++ b/advanced_topics/08_fslpy.md
@@ -188,8 +188,8 @@ stddir = op.expandvars('${FSLDIR}/data/standard/')
# load a FSL image - the file
# suffix is optional, just like
# in real FSL-land!
-img = Image(op.join(stddir, 'MNI152_T1_1mm'))
-print(img)
+std1mm = Image(op.join(stddir, 'MNI152_T1_1mm'))
+print(std1mm)
```
@@ -200,7 +200,7 @@ You can create an `Image` from an existing `nibabel` image:
# load a nibabel image, and
# convert it into an FSL image
nibimg = nib.load(op.join(stddir, 'MNI152_T1_1mm.nii.gz'))
-img = Image(nibimg)
+std1mm = Image(nibimg)
```
@@ -208,15 +208,26 @@ Or you can create an `Image` from a `numpy` array:
```
-data = np.zeros((100, 100, 100))
+data = np.zeros((182, 218, 182))
img = Image(data, xform=np.eye(4))
```
+If you have generated some data from another `Image` (or from a
+`nibabel.Nifti1Image`) you can use the `header` option to set
+the header information on the new image:
+
+
+```
+img = Image(data, header=std1mm.header)
+```
+
+
You can save an image to file via the `save` method:
```
-img.save('empty.nii.gz')
+img.save('empty')
+!ls
```
--
GitLab