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4 | 4 | Python in NeuroImaging
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5 | 5 | ======================
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6 | 6 |
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7 |
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8 | 7 | Please provide for every sub-project a brief Description, list of
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9 | 8 | Features, some nice figure if you have any. Hopefully eventually we
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10 | 9 | get enough of tasty materials someone could compose into a flier.
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@@ -49,13 +48,41 @@ NiBabel
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49 | 48 | ~~~~~~~
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50 | 49 | http://nipy.org/nibabel
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51 | 50 |
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| 51 | +.. figure:: ../pics/reggie.png |
| 52 | + :alt: nibabel |
| 53 | + :align: right |
| 54 | + :figwidth: 35% |
| 55 | + |
| 56 | +Nibabel provides read and write access to some common medical and neuroimaging |
| 57 | +file formats, including: ANALYZE_ (plain, SPM99, SPM2), GIFTI_, NIfTI1_, MINC_, |
| 58 | +as well as PAR/REC. NiBabel is the successor of PyNIfTI_. |
| 59 | + |
| 60 | +.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm |
| 61 | +.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ |
| 62 | +.. _MINC: http://wiki.bic.mni.mcgill.ca/index.php/MINC |
| 63 | +.. _PyNIfTI: http://niftilib.sourceforge.net/pynifti/ |
| 64 | +.. _GIFTI: http://www.nitrc.org/projects/gifti |
| 65 | + |
| 66 | +The various image format classes give full or selective access to header (meta) |
| 67 | +information and access to the image data is made available via NumPy arrays. |
| 68 | + |
52 | 69 | Analysis
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53 | 70 | --------
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54 | 71 |
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55 | 72 | NiPy
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56 | 73 | ~~~~
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57 | 74 | http://nipy.org/nipy
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58 | 75 |
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| 76 | +NIPY has algorithms for the analysis of neuroimaging data including: |
| 77 | + |
| 78 | +* General linear model statistical analysis |
| 79 | +* Combined slice time correction and motion correction |
| 80 | +* General image registration routines with flexible cost functions, optimizers |
| 81 | + and resampling schemes |
| 82 | +* Image segmentation |
| 83 | +* Basic visualization of results in 2D and 3D |
| 84 | +* Basic time series diagnostics |
| 85 | +* Clustering and activation pattern analysis across subjects |
59 | 86 |
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60 | 87 | Nipype
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61 | 88 | ~~~~~~
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91 | 118 | ~~~~
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92 | 119 | http://nipy.org/dipy
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93 | 120 |
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| 121 | +.. figure:: ../pics/dipy-banner.png |
| 122 | + :alt: nibabel |
| 123 | + :align: right |
| 124 | + :figwidth: 35% |
| 125 | + |
| 126 | +Dipy is an international, free and open soure software project for |
| 127 | +diffusion magnetic resonance imaging analysis. |
| 128 | + |
| 129 | +Dipy is multiplatform and will run under any standard operating system such as |
| 130 | +*Windows*, *Linux*, *Mac OS X*. |
| 131 | + |
| 132 | +Just some of our **state-of-the-art** applications are: |
| 133 | + |
| 134 | +- Reconstruction algorithms e.g. GQI, DTI |
| 135 | +- Tractography generation algorithms e.g. EuDX |
| 136 | +- Intelligent downsampling of tracks |
| 137 | +- Ultra fast tractography clustering |
| 138 | +- Resampling datasets with anisotropic voxels to isotropic |
| 139 | +- Visualizing multiple brains simultaneously |
| 140 | +- Finding track correspondence between different brains |
| 141 | +- Warping tractographies into another space e.g. MNI space |
| 142 | +- Reading many different file formats e.g. Trackvis or Nifti |
| 143 | +- Dealing with huge tractographies without memory restrictions |
| 144 | +- Playing with datasets interactively without storing |
| 145 | +- And much more and even more to come in next releases |
| 146 | + |
94 | 147 |
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95 | 148 | NiTime
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96 | 149 | ~~~~~~
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