Visualizing_nifti_files.md

contrib/plotting-visualization/Visualizing_nifti_files.md

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+## NIfTI Files
+Neuroimaging Informatics Technology Initiative is a data format for storage. Functional Magnetic Resonance Imaging (fMRI) and other medical images.
+## In this, we'll be using different packages:
+1. Matplotlib
+2. Nibabel: It gives access to a variety of imaging formats, it provides a common interface for various formats produced by different scanners.
+
+## Various Methods for viewing a NIfTI file
+### 1. Load NIfTI file
+```
+brain_vol = nib.load("") #Enter the path to NIfTI file here
+type(brain_vol)
+```
+### 2. View Metadata
+```
+print(brain_vol.header)
+```
+### Output
+```
+<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
+sizeof_hdr      : 348
+data_type       : b''
+db_name         : b''
+extents         : 0
+session_error   : 0
+regular         : b'r'
+dim_info        : 54
+dim             : [  3 192 256 256   1   1   1   1]
+intent_p1       : 0.0
+intent_p2       : 0.0
+intent_p3       : 0.0
+intent_code     : none
+datatype        : int16
+bitpix          : 16
+slice_start     : 0
+pixdim          : [1.  1.  1.  1.  2.3 0.  0.  0. ]
+vox_offset      : 0.0
+scl_slope       : nan
+scl_inter       : nan
+slice_end       : 0
+slice_code      : unknown
+xyzt_units      : 10
+cal_max         : 0.0
+cal_min         : 0.0
+slice_duration  : 0.0
+toffset         : 0.0
+glmax           : 0
+glmin           : 0
+descrip         : b'TE=2.7;Time=150734.828;phase=1'
+aux_file        : b''
+qform_code      : scanner
+sform_code      : scanner
+quatern_b       : 0.00042526424
+quatern_c       : -0.027039066
+quatern_d       : 0.01571919
+qoffset_x       : -81.5222
+qoffset_y       : -130.72974
+qoffset_z       : -144.47054
+srow_x          : [ 9.9804670e-01 -3.1445995e-02 -5.4038301e-02 -8.1522202e+01]
+srow_y          : [ 3.1400096e-02  9.9950546e-01 -1.7001767e-03 -1.3072974e+02]
+srow_z          : [ 5.4065209e-02  4.7863640e-08  9.9853742e-01 -1.4447054e+02]
+intent_name     : b''
+magic           : b'n+1'
+```
+### 3. Access data in the NIfTI object
+```
+brain_vol_data = brain_vol.get_fdata()
+type(brain_vol_data)
+```
+### Output
+```
+numpy.ndarray
+```
+### Dimensions of the image
+```
+brain_vol_data.shape
+```
+### Output
+```
+(192, 256, 256)
+```
+### 4. Visualize a Slice
+```
+plt.imshow(brain_vol_data[96], cmap='bone')
+plt.axis('off')
+plt.show()
+```
+
+
+
+