tashrifbillah

from util import *
from rish import rish
N_shm=2

def approxSignal(imgPath, maskPath):

    directory = os.path.dirname(imgPath)
    inPrefix = imgPath.split('.nii')[0]
    prefix = os.path.split(inPrefix)[-1]
    outPrefix = os.path.join(directory, 'harm', prefix)

tashrifbillah

def single_pass(InputImage, scale):

    temp_image= InputImage.copy()

    for s in range(scale,0,-1):
        temp_image= single_scale(temp_image, s)

    temp_image= findLargestConnectMask(temp_image)

    OutputImage= temp_image

tashrifbillah

antsApplyTransforms -d 3 -i /rds/general/user/fmoro/home/bioaxlive/Controls/DTI/London/COB_I078/harm_trial_4/COB_I078_mask.nii.gz \
-o /rds/general/user/fmoro/home/bioaxlive/Controls/DTI/London/COB_I078/harm_trial_4/COB_I078_mask_resampledWarped.nii.gz \
-r /rds/general/user/fmoro/home/template_lau4/template0.nii.gz \
-t /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*[!Inverse]Warp.nii.gz \
-t /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*GenericAffine.mat

# if the above does not work, do
ls /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*[!Inverse]Warp.nii.gz
ls /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*GenericAffine.mat
# and replace the last two lines in the former block with absolute paths obtained from the latter

tashrifbillah

#!/usr/bin/env python

import dash
import dash_html_components as html
import dash_core_components as dcc
from dash_table import DataTable
from dash_table.Format import Format
import pandas as pd

app = dash.Dash(__name__)

tashrifbillah

Windows and Linux users are accustomed to standard layout keyboard. When they have to work on a MacBook, the absence of some important keys may be felt. Here I put together the equivalent MacBook key sequences for the absent keys:

Key	MS word	Browser	Terminal	Vi / Vim
Home	fn + ←	command + ←	shift + fn + ←	fn + ←
End	fn + →	command + →	shift + fn + →	fn + →
* Page Up	fn + ↑
* Page Down	fn + ↓
* Delete	fn + delete
* Backspace	delete

tashrifbillah

# run as python shape_check.py

from conversion import read_cases
import numpy as np
from nibabel import load
from os.path import isfile

# copy this script to DIAGNOSE_CTE_U01/derivatives/pnlpipe and run from there
# adjust caselist if necessary
cases=read_cases('../../caselists/Caselist_ALL.txt')

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# copy this script in the following directory and run from there
# cd DIAGNOSE_CTE_U01/derivatives/pnlpipe
# run as sh fix_bbox.sh

for c in $(cat incongruous_cases.txt)
do
  mask_name=sub-${c}/ses-01/dwi/sub-${c}_ses-01_desc-dwiXcCNNQc_mask.nii.gz
  bse_name=sub-${c}/ses-01/dwi/sub-${c}_ses-01_desc-dwiXc_bse.nii.gz
  
  echo $c

tashrifbillah

#!/usr/bin/env python

from luigi import build, Task, LocalTarget, FloatParameter
from luigi.util import requires
import numpy as np

class TaskA(Task):

    a= FloatParameter(default=round(np.random.rand(),3))

tashrifbillah

#!/usr/bin/env python

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.ticker as ticker
import matplotlib.pyplot as plt
import numpy as np
from numpy.random import rand
from itertools import product, combinations
from conversion import read_bvecs, read_bvals, write_bvals
from os.path import abspath, splitext, basename

tashrifbillah

#!/usr/bin/env python

import dash
import dash_html_components as html
import dash_core_components as dcc
from dash.dependencies import Input, Output

external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']

app = dash.Dash(__name__, external_stylesheets=external_stylesheets)