| import numpy as np | |
| import matplotlib.pyplot as plt | |
| from matplotlib.widgets import LassoSelector | |
| from matplotlib import path | |
| fig = plt.figure() | |
| ax1 = fig.add_subplot(121) | |
| ax1.set_title('lasso selection:') | |
| ax1.plot() | |
| ax1.set_xlim([0, 10]) |
| """Convert minc to nifti format.""" | |
| import os | |
| import numpy as np | |
| from nibabel import load, save, Nifti1Image | |
| minc = load("/path/to/file.mnc.gz") | |
| basename = minc.get_filename().split(os.extsep, 1)[0] | |
| affine = np.array([[0, 0, 1, 0], |
| import numpy as np | |
| cimport numpy as np | |
| cimport cython | |
| @cython.boundscheck(False) | |
| @cython.wraparound(False) | |
| cpdef cython_lstsqr(x_ary, y_ary): | |
| """ Computes the least-squares solution to a linear matrix equation. """ | |
| cdef double x_avg, y_avg, var_x, cov_xy,\ | |
| slope, y_interc |
| """Add freesurfer labels similar to 'fslmaths -add'. | |
| Use an .mgh file to read relevant information such as headers or number of | |
| vertices. | |
| Note: Freesurfer operations can be performed on .mgh format without | |
| getting unrecognized data type error. | |
| """ | |
| import numpy as np |
| """Example for sorting 4D nifti data.""" | |
| import numpy as np | |
| import os | |
| from nibabel import load, save, Nifti1Image | |
| from __future__ import division | |
| nii = load('/path/to/your/4D_nifti_file.nii.gz') | |
| basename = nii.get_filename().split(os.extsep, 1)[0] | |
| niiHeader = nii.header |
Some terms
Anaconda: full distributor for python packages, uses only conda.
Miniconda: stripped down version of anaconda containing only the bare minimum packages (can use both conda and pip).
conda: a package manager.
pip: another package manager.
To be able to run Psychopy(1.84.2) from Conda with Spyder you need to follow these steps:
| """Pyusb with Griffin Powermate. | |
| Linux notes: | |
| On Debian 8 it requires admin rights to access the powermate device. | |
| The script can be tested via activating superuser and the virtual | |
| environment with pyusb and calling the script. | |
| Usage notes: | |
| dev.read returns the following values in an array: | |
| 0: button state (0 not pressed, 1 pressed) |
| """Test Griffin Powermate library using pywinusb.""" | |
| from griffin_powermate import GriffinPowermate | |
| def rotation_listener(data): | |
| """Print powermate input only for rotation.""" | |
| global dial_click | |
| if data[1] == 1 : | |
| dial_click = True |
| % Convert VMR files with uint16 precision (.v16) using neuroelf. | |
| % | |
| % v16 files are better than vmr files for nifti conversion because | |
| % because the intensity values are not limited to the small range of | |
| % 0 to 255 integers. | |
| % | |
| % http://neuroelf.net/ | |
| [fileName, pathName] = uigetfile('.v16'); | |
| vmr = xff(fullfile(pathName, fileName)); |
| // Batch script for cretaing FMR files from renamed dicom files (.dcm). | |
| // | |
| // You need to create the subfolders in the main data path beforehand. | |
| // For instance: /path/to/your/subject/RUN_1 | |
| // /path/to/your/subject/RUN_2 | |
| // ... | |
| // | |
| // For more information, check the scripting guide: | |
| // http://support.brainvoyager.com/automation-aamp-development/46-writing-scripts/133-scripting-reference-guide.html |