From 30e8c66178e66e363a1ae721dcc960265302797b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 24 Mar 2020 22:22:01 +0000
Subject: [PATCH] RF: little tweaks
---
advanced_topics/08_fslpy.ipynb | 16 +++++++++++-----
advanced_topics/08_fslpy.md | 12 +++++++++---
2 files changed, 20 insertions(+), 8 deletions(-)
diff --git a/advanced_topics/08_fslpy.ipynb b/advanced_topics/08_fslpy.ipynb
index acda784..546c1f7 100644
--- a/advanced_topics/08_fslpy.ipynb
+++ b/advanced_topics/08_fslpy.ipynb
@@ -67,7 +67,8 @@
"import nibabel as nib\n",
"import numpy as np\n",
"import warnings\n",
- "warnings.filterwarnings(\"ignore\")"
+ "warnings.filterwarnings(\"ignore\")\n",
+ "np.set_printoptions(suppress=True, precision=4)"
]
},
{
@@ -432,7 +433,7 @@
"\n",
"* The\n",
" [`fsl.data.bitmap.Bitmap`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.bitmap.html)\n",
- " class can be used to load a bitmap image (e.g. `jpg, `png`, etc) and\n",
+ " class can be used to load a bitmap image (e.g. `jpg`, `png`, etc) and\n",
" convert it to a NIfTI image.\n",
"* The\n",
" [`fsl.data.dicom.DicomImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dicom.html)\n",
@@ -659,7 +660,8 @@
"# To combine affines together, we\n",
"# have to list them in reverse -\n",
"# linear algebra is *weird*.\n",
- "funcvox2mni = concat(fsl2mni, func2std, vox2fsl)"
+ "funcvox2mni = concat(fsl2mni, func2std, vox2fsl)\n",
+ "print(funcvox2mni)"
]
},
{
@@ -915,7 +917,7 @@
"metadata": {},
"outputs": [],
"source": [
- "seedstruc = struc2std.transform([seedmni], 'world', 'voxel')[0]\n",
+ "seedstruc = struc2std.transform(seedmni, 'world', 'voxel')\n",
"seedfunc = transform(seedstruc, struc2func)\n",
"\n",
"print('Seed location in MNI coordinates: ', seedmni)\n",
@@ -1015,7 +1017,7 @@
"metadata": {},
"outputs": [],
"source": [
- "from fsl.wrappers import bet, robustfov, LOAD\n",
+ "from fsl.wrappers import robustfov\n",
"\n",
"robustfov('08_fslpy/bighead', 'bighead_cropped')\n",
"\n",
@@ -1059,6 +1061,8 @@
"metadata": {},
"outputs": [],
"source": [
+ "from fsl.wrappers import bet\n",
+ "\n",
"bet('bighead_cropped', 'bighead_cropped_brain', f=0.3, m=True, s=True)\n",
"\n",
"render('bighead_cropped -b 40 '\n",
@@ -1132,6 +1136,8 @@
"metadata": {},
"outputs": [],
"source": [
+ "from fsl.wrappers import LOAD\n",
+ "\n",
"cropped = Image('bighead_cropped')\n",
"\n",
"# The loaded result is called \"output\",\n",
diff --git a/advanced_topics/08_fslpy.md b/advanced_topics/08_fslpy.md
index b8fb3b2..043dfab 100644
--- a/advanced_topics/08_fslpy.md
+++ b/advanced_topics/08_fslpy.md
@@ -57,6 +57,7 @@ import nibabel as nib
import numpy as np
import warnings
warnings.filterwarnings("ignore")
+np.set_printoptions(suppress=True, precision=4)
```
@@ -321,7 +322,7 @@ corresponding `nibabel` types:
* The
[`fsl.data.bitmap.Bitmap`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.bitmap.html)
- class can be used to load a bitmap image (e.g. `jpg, `png`, etc) and
+ class can be used to load a bitmap image (e.g. `jpg`, `png`, etc) and
convert it to a NIfTI image.
* The
[`fsl.data.dicom.DicomImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dicom.html)
@@ -496,6 +497,7 @@ from fsl.transform.affine import concat
# have to list them in reverse -
# linear algebra is *weird*.
funcvox2mni = concat(fsl2mni, func2std, vox2fsl)
+print(funcvox2mni)
```
> In the next section we will use the
@@ -668,7 +670,7 @@ MNI152 space into structural space:
```
-seedstruc = struc2std.transform([seedmni], 'world', 'voxel')[0]
+seedstruc = struc2std.transform(seedmni, 'world', 'voxel')
seedfunc = transform(seedstruc, struc2func)
print('Seed location in MNI coordinates: ', seedmni)
@@ -744,7 +746,7 @@ corresponding tool via the command-line:
```
-from fsl.wrappers import bet, robustfov, LOAD
+from fsl.wrappers import robustfov
robustfov('08_fslpy/bighead', 'bighead_cropped')
@@ -780,6 +782,8 @@ positional arguments, and pass the additional options as keyword arguments:
```
+from fsl.wrappers import bet
+
bet('bighead_cropped', 'bighead_cropped_brain', f=0.3, m=True, s=True)
render('bighead_cropped -b 40 '
@@ -837,6 +841,8 @@ files produced by the tool automatically loaded into memory for you:
```
+from fsl.wrappers import LOAD
+
cropped = Image('bighead_cropped')
# The loaded result is called "output",
--
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