Using tractography function in pipeline to generate structure tensors

Import the main analysis module and tractography module. Use the analysis module to download a raw brain of interest, then use the tractography function "nii_to_tiff_stack" to save a .nii as a TIFF stack.



In [1]:

    
import tractography as tract



In [2]:

    
import analysis3 as a3



In [3]:

    
output = a3.get_raw_brain("s275", "userToken.pem", save = True)



In [4]:

    
tract.nii_to_tiff_stack("s275_raw.nii", "s275")



In [5]:

    
data = tract.tiff_stack_to_array("s275_TIFFs/")









    



(62, 51, 1114)

From there, run the generate_FSL_structure_tensor code to save a copy of the FSL structure tensor.

Note that the value can also be directly used from the function.



In [6]:

    
tract.generate_FSL_structure_tensor(data, "s275")









    



Start DoG Sigma on 1
Start Gauss Sigma with gausigma = 2.3
Generating Gaussian kernel...
Blurring gradient products...
Saving a copy for this Gaussian sigma...
Completed computing structure tensor on s275!






    Out[6]:





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In [ ]: