From cbc72ef9d3c36fba38480709de60ec8ba06f578c Mon Sep 17 00:00:00 2001 From: Niyonika Gaur <83643952+niyonikagaur@users.noreply.github.com> Date: Sun, 2 Jun 2024 11:31:01 +0530 Subject: [PATCH] Visualizing_nifti_files.md --- .../Visualizing_nifti_files.md | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 contrib/plotting-visualization/Visualizing_nifti_files.md diff --git a/contrib/plotting-visualization/Visualizing_nifti_files.md b/contrib/plotting-visualization/Visualizing_nifti_files.md new file mode 100644 index 0000000..4baaca3 --- /dev/null +++ b/contrib/plotting-visualization/Visualizing_nifti_files.md @@ -0,0 +1,90 @@ +## 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 +``` + 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() +``` + + + +