FSL - Brain Extraction Tool(BET) Quality Check

This script was created when the BET performed realy poorly on subjects of ABIDE. It is a very simple script that does the following:

Read the brain nifti files using the bash's find command and save it to a file as -
```
find . -name "sub-*.nii.gz" > filename.txt
```
Read the file to extract all the filenames.
Count the number of brain voxels in each nifti file.
Then find the number of brains whose number brain voxels are some specific standard deviations away from the mean.

I used another metric that didn't work

Count the voxels that doesnot lie inside the standard mask.
This didn't work as ater the transformation to the standard space the brains were totally skewed but lied inside the standard mask.



In [ ]:

    
import numpy as np
import subprocess
import os
from os.path import join as opj
import re
import nibabel as nib



In [56]:

    
# paths = np.genfromtxt('/home1/varunk/results_again_again/anat_file_paths.txt', dtype='str') #Didn't work

# paths = np.genfromtxt('/home1/varunk/results_again_again/skullstrip_anat.txt', dtype='str') 

paths = np.genfromtxt('/home1/varunk/results_again_again/bet_resample_reg_brain_paths.txt', dtype='str')

# paths = np.genfromtxt('/home1/varunk/results_again_again/bet_resample_brain_paths.txt', dtype='str')
paths = np.sort(paths)
save_destination = '/home1/varunk/results_again_again/registered_anat_qc/'
if not os.path.exists(save_destination):
    os.mkdir(save_destination)
    
os.chdir(save_destination)



In [57]:

    
# print(np.sort(paths)[0:10])
paths









    Out[57]:





array([ './_subject_id_0050002/anat2std_reg/sub-0050002_T1w_brain_resample_flirt.nii',
       './_subject_id_0050003/anat2std_reg/sub-0050003_T1w_brain_resample_flirt.nii',
       './_subject_id_0050004/anat2std_reg/sub-0050004_T1w_brain_resample_flirt.nii',
       ...,
       './_subject_id_0051585/anat2std_reg/sub-0051585_T1w_brain_resample_flirt.nii',
       './_subject_id_0051606/anat2std_reg/sub-0051606_T1w_brain_resample_flirt.nii',
       './_subject_id_0051607/anat2std_reg/sub-0051607_T1w_brain_resample_flirt.nii'],
      dtype='<U75')

Metric: Number of non zero voxels (Brain Voxels)



In [59]:

    
# paths = paths[0:3]
res_voxels = []
for path in paths:
    base_dir = '/home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg'
    anat_path = base_dir + path[1:]
    print(anat_path)
    sub_id_extracted = re.search('.+_subject_id_(\d+)', anat_path).group(1)
#     out_file = 'sub_' + sub_id_extracted + '_residual'
    
    res_file = opj(os.getcwd(),out_file)
    proc = subprocess.Popen(['fslstats', anat_path, '-V'], 
                             stdout=subprocess.PIPE)
    voxels = int((proc.communicate()[0]).decode("utf-8").split(' ')[0])
    res_voxels.append(voxels)









    



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In [60]:

    
res_voxels



In [61]:

    
%matplotlib inline
import matplotlib.pyplot as plt

bins = np.arange(min(res_voxels), max(res_voxels), 500) # fixed bin size

res = plt.hist(res_voxels, 
         bins=bins, 
         alpha=0.5, 
         color='#887E43',
         label='Defender')

np.mean(res_voxels),np.std(res_voxels)



In [66]:

    
#number_of_outliers = 
(res_voxels > 10.0*np.std(res_voxels)).sum()









    Out[66]:





1102



In [68]:

    
paths[np.where((res_voxels > 20.0*np.std(res_voxels)) == True)]









    Out[68]:





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       './_subject_id_0051367/anat2std_reg/sub-0051367_T1w_brain_resample_flirt.nii',
       './_subject_id_0051368/anat2std_reg/sub-0051368_T1w_brain_resample_flirt.nii',
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       './_subject_id_0051370/anat2std_reg/sub-0051370_T1w_brain_resample_flirt.nii',
       './_subject_id_0051371/anat2std_reg/sub-0051371_T1w_brain_resample_flirt.nii',
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       './_subject_id_0051493/anat2std_reg/sub-0051493_T1w_brain_resample_flirt.nii',
       './_subject_id_0051556/anat2std_reg/sub-0051556_T1w_brain_resample_flirt.nii',
       './_subject_id_0051557/anat2std_reg/sub-0051557_T1w_brain_resample_flirt.nii',
       './_subject_id_0051558/anat2std_reg/sub-0051558_T1w_brain_resample_flirt.nii',
       './_subject_id_0051559/anat2std_reg/sub-0051559_T1w_brain_resample_flirt.nii',
       './_subject_id_0051560/anat2std_reg/sub-0051560_T1w_brain_resample_flirt.nii',
       './_subject_id_0051561/anat2std_reg/sub-0051561_T1w_brain_resample_flirt.nii',
       './_subject_id_0051562/anat2std_reg/sub-0051562_T1w_brain_resample_flirt.nii',
       './_subject_id_0051563/anat2std_reg/sub-0051563_T1w_brain_resample_flirt.nii',
       './_subject_id_0051564/anat2std_reg/sub-0051564_T1w_brain_resample_flirt.nii',
       './_subject_id_0051565/anat2std_reg/sub-0051565_T1w_brain_resample_flirt.nii',
       './_subject_id_0051566/anat2std_reg/sub-0051566_T1w_brain_resample_flirt.nii',
       './_subject_id_0051567/anat2std_reg/sub-0051567_T1w_brain_resample_flirt.nii',
       './_subject_id_0051568/anat2std_reg/sub-0051568_T1w_brain_resample_flirt.nii',
       './_subject_id_0051569/anat2std_reg/sub-0051569_T1w_brain_resample_flirt.nii',
       './_subject_id_0051570/anat2std_reg/sub-0051570_T1w_brain_resample_flirt.nii',
       './_subject_id_0051571/anat2std_reg/sub-0051571_T1w_brain_resample_flirt.nii',
       './_subject_id_0051572/anat2std_reg/sub-0051572_T1w_brain_resample_flirt.nii',
       './_subject_id_0051573/anat2std_reg/sub-0051573_T1w_brain_resample_flirt.nii',
       './_subject_id_0051574/anat2std_reg/sub-0051574_T1w_brain_resample_flirt.nii',
       './_subject_id_0051575/anat2std_reg/sub-0051575_T1w_brain_resample_flirt.nii',
       './_subject_id_0051576/anat2std_reg/sub-0051576_T1w_brain_resample_flirt.nii',
       './_subject_id_0051577/anat2std_reg/sub-0051577_T1w_brain_resample_flirt.nii',
       './_subject_id_0051578/anat2std_reg/sub-0051578_T1w_brain_resample_flirt.nii',
       './_subject_id_0051579/anat2std_reg/sub-0051579_T1w_brain_resample_flirt.nii',
       './_subject_id_0051580/anat2std_reg/sub-0051580_T1w_brain_resample_flirt.nii',
       './_subject_id_0051582/anat2std_reg/sub-0051582_T1w_brain_resample_flirt.nii',
       './_subject_id_0051583/anat2std_reg/sub-0051583_T1w_brain_resample_flirt.nii',
       './_subject_id_0051584/anat2std_reg/sub-0051584_T1w_brain_resample_flirt.nii',
       './_subject_id_0051585/anat2std_reg/sub-0051585_T1w_brain_resample_flirt.nii',
       './_subject_id_0051606/anat2std_reg/sub-0051606_T1w_brain_resample_flirt.nii',
       './_subject_id_0051607/anat2std_reg/sub-0051607_T1w_brain_resample_flirt.nii'],
      dtype='<U75')



In [ ]:



In [23]:

    
np.mean(res_voxels),np.std(res_voxels)









    Out[23]:





(64565.743194192379, 7832.0396289753444)



In [76]:

    
#number_of_outliers = 
s = 3
(res_voxels > np.mean(res_voxels) + s*np.std(res_voxels)).sum(), (res_voxels < np.mean(res_voxels) - s*np.std(res_voxels)).sum()









    Out[76]:





(3, 1)



In [25]:

    
# index of outliers
np.where((res_voxels > 6.0*np.std(res_voxels)) == True)









    Out[25]:





(array([   0,    1,    2, ..., 1099, 1100, 1101]),)



In [27]:

    
# Subjects that are outliers
paths[np.where((res_voxels > 15.0*np.std(res_voxels)) == True)]









    Out[27]:





array(['./_subject_id_0050694/resample_anat/sub-0050694_T1w_brain_resample.nii',
       './_subject_id_0050697/resample_anat/sub-0050697_T1w_brain_resample.nii',
       './_subject_id_0051263/resample_anat/sub-0051263_T1w_brain_resample.nii',
       './_subject_id_0051296/resample_anat/sub-0051296_T1w_brain_resample.nii'],
      dtype='<U70')



In [49]:

    
# Subjects that are outliers
set(paths[np.where((res_voxels > 12.0*np.std(res_voxels)) == True)])









    Out[49]:





{'./_subject_id_0050694/resample_anat/sub-0050694_T1w_brain_resample.nii',
 './_subject_id_0050697/resample_anat/sub-0050697_T1w_brain_resample.nii',
 './_subject_id_0050746/resample_anat/sub-0050746_T1w_brain_resample.nii',
 './_subject_id_0051263/resample_anat/sub-0051263_T1w_brain_resample.nii',
 './_subject_id_0051296/resample_anat/sub-0051296_T1w_brain_resample.nii',
 './_subject_id_0051312/resample_anat/sub-0051312_T1w_brain_resample.nii'}



In [53]:

    
# Subjects that are outliers
set(paths[np.where((res_voxels > 11.0*np.std(res_voxels)) == True)]) -  set(paths[np.where((res_voxels > 12.0*np.std(res_voxels)) == True)])









    Out[53]:





{'./_subject_id_0050603/resample_anat/sub-0050603_T1w_brain_resample.nii',
 './_subject_id_0050626/resample_anat/sub-0050626_T1w_brain_resample.nii'}



In [54]:

    
set(paths[np.where((res_voxels > 10.0*np.std(res_voxels)) == True)]) - set(paths[np.where((res_voxels > 11.0*np.std(res_voxels)) == True)])









    Out[54]:





{'./_subject_id_0050007/resample_anat/sub-0050007_T1w_brain_resample.nii',
 './_subject_id_0050011/resample_anat/sub-0050011_T1w_brain_resample.nii',
 './_subject_id_0050016/resample_anat/sub-0050016_T1w_brain_resample.nii',
 './_subject_id_0050019/resample_anat/sub-0050019_T1w_brain_resample.nii',
 './_subject_id_0050132/resample_anat/sub-0050132_T1w_brain_resample.nii',
 './_subject_id_0050136/resample_anat/sub-0050136_T1w_brain_resample.nii',
 './_subject_id_0050239/resample_anat/sub-0050239_T1w_brain_resample.nii',
 './_subject_id_0050244/resample_anat/sub-0050244_T1w_brain_resample.nii',
 './_subject_id_0050432/resample_anat/sub-0050432_T1w_brain_resample.nii',
 './_subject_id_0050489/resample_anat/sub-0050489_T1w_brain_resample.nii',
 './_subject_id_0050607/resample_anat/sub-0050607_T1w_brain_resample.nii',
 './_subject_id_0050655/resample_anat/sub-0050655_T1w_brain_resample.nii',
 './_subject_id_0050659/resample_anat/sub-0050659_T1w_brain_resample.nii',
 './_subject_id_0050666/resample_anat/sub-0050666_T1w_brain_resample.nii',
 './_subject_id_0050800/resample_anat/sub-0050800_T1w_brain_resample.nii',
 './_subject_id_0050972/resample_anat/sub-0050972_T1w_brain_resample.nii',
 './_subject_id_0051133/resample_anat/sub-0051133_T1w_brain_resample.nii',
 './_subject_id_0051213/resample_anat/sub-0051213_T1w_brain_resample.nii',
 './_subject_id_0051316/resample_anat/sub-0051316_T1w_brain_resample.nii',
 './_subject_id_0051464/resample_anat/sub-0051464_T1w_brain_resample.nii',
 './_subject_id_0051470/resample_anat/sub-0051470_T1w_brain_resample.nii',
 './_subject_id_0051472/resample_anat/sub-0051472_T1w_brain_resample.nii'}



In [55]:

    
paths[np.where((res_voxels > 10.0*np.std(res_voxels)) == True)].shape









    Out[55]:





(30,)



In [33]:

    
subject_ids_corrupted = [] 
for path in paths[np.where((res_voxels > 6.0*np.std(res_voxels)) == True)]:
    sub_id_extracted = re.search('.+_subject_id_(\d+)', path).group(1)
    subject_ids_corrupted.append(str(int(sub_id_extracted)))



In [34]:

    
subject_ids_corrupted









    Out[34]:





['50002',
 '50007',
 '50009',
 '50011',
 '50015',
 '50016',
 '50017',
 '50019',
 '50020',
 '50026',
 '50045',
 '50047',
 '50050',
 '50058',
 '50060',
 '50104',
 '50110',
 '50118',
 '50121',
 '50132',
 '50133',
 '50136',
 '50137',
 '50155',
 '50184',
 '50197',
 '50234',
 '50239',
 '50244',
 '50246',
 '50263',
 '50278',
 '50323',
 '50329',
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In [ ]:

    
# Find the error:
import nibabel as nib

res_voxels = []

res_file = '/home1/varunk/results_again_again/registered_anat_qc/0050977_residual.nii.gz'
proc = subprocess.Popen(['fslstats', res_file, '-V'], 
                         stdout=subprocess.PIPE)
voxels = int((proc.communicate()[0]).decode("utf-8").split(' ')[0])
res_voxels.append(voxels)



In [ ]:

    
res_voxels



In [ ]:

    
!fslmaths /home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg/_subject_id_0050977/skullStrip/sub-0050977_T1w_resample_brain.nii.gz -mul /home1/varunk/results_again_again/registered_anat_qc/mask_inverted.nii.gz 0050977_residual



In [ ]:

    
paths = paths[0:3]
for path in paths:
    base_dir = '/home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg'
    anat_path = base_dir + path[1:]
    print(anat_path)



In [ ]:

    
# (stddata[0]).decode("utf-8").split(' ')[0]



In [ ]:

The metric that did not work.

It could not actually figure out the bad brains

Create the inverted mask



In [58]:

    
mask = '/home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg/resample_mni/MNI152_T1_2mm_brain_resample_mask.nii.gz'

proc = subprocess.Popen(['fslmaths', mask, '-mul', '-1', '-add' ,'1', 'mask_inverted'], 
                         stdout=subprocess.PIPE)
stdoutdata= proc.communicate()
print("The commandline is: {}".format(subprocess.list2cmdline(proc.args)))

cwd = os.getcwd()

mask_inverted_path = opj(cwd, 'mask_inverted.nii.gz')









    



The commandline is: fslmaths /home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg/resample_mni/MNI152_T1_2mm_brain_resample_mask.nii.gz -mul -1 -add 1 mask_inverted



In [6]:

    
# /home1/varunk/results_again_again/registered_anat_qc/mask_inverted.nii.gz



In [7]:

    
# paths



In [8]:

    
%%time
# paths = paths[0:3]
res_voxels = []
for path in paths:
    base_dir = '/home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg'
    anat_path = base_dir + path[1:]
#     print(anat_path)
    sub_id_extracted = re.search('.+_subject_id_(\d+)', anat_path).group(1)
    out_file = 'sub_' + sub_id_extracted + '_residual'
    proc = subprocess.Popen(['fslmaths', anat_path, '-mul', mask_inverted_path, out_file], 
                         stdout=subprocess.PIPE)
    stdoutdata= proc.communicate()
    print("The command executed is: {}".format(subprocess.list2cmdline(proc.args)))
#     print('Created the residual file for Subject', sub_id_extracted)

    

    res_file = opj(os.getcwd(),out_file)
    proc = subprocess.Popen(['fslstats', res_file, '-V'], 
                             stdout=subprocess.PIPE)
    voxels = int((proc.communicate()[0]).decode("utf-8").split(' ')[0])
    res_voxels.append(voxels)
    
#     print(stdoutdata)
    
# , stderrdata ,    
# , stderr=subprocess.STDOUT









    



The command executed is: fslmaths /home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg/_subject_id_0050002/anat2std_reg/sub-0050002_T1w_resample_brain_flirt.nii -mul /home1/varunk/results_again_again/registered_anat_qc/mask_inverted.nii.gz sub_0050002_residual






    



---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<timed exec> in <module>()

ValueError: invalid literal for int() with base 10: ''



In [8]:

    
!fslmaths /home1/varunk/results_again_again/ABIDE1_Preprocess/motion_correction_bet/coreg_reg/_subject_id_0050002/skullStrip/sub-0050002_T1w_resample_brain.nii.gz -mul /home1/varunk/results_again_again/registered_anat_qc/mask_inverted.nii.gz sub_0050002_residual









    



WARNING:: Inconsistent orientations for individual images in pipeline!
          Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!

Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)



In [9]:

    
res_voxels









    Out[9]:





[]



In [10]:

    
np.mean(res_voxels),np.std(res_voxels)









    



/root/anaconda3/lib/python3.6/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide
  arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)






    Out[10]:





(nan, nan)



In [11]:

    
#number_of_outliers = 
(res_voxels > 6*np.std(res_voxels)).sum()









    



/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide
  arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)






    Out[11]:





0



In [12]:

    
# index of outliers
np.where((res_voxels > 6*np.std(res_voxels)) == True)









    



/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide
  arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)






    Out[12]:





(array([], dtype=int64),)



In [26]:

    
# Subjects that are outliers
paths[np.where((res_voxels > 6*np.std(res_voxels)) == True)]









    



/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide
  arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/root/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)






    Out[26]:





array([],
      dtype='<U70')



In [ ]: