Ryan Zurrin RyanZurrin

## disable_update_instructions.md

      
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                RyanZurrin
                / disable_update_instructions.md
            
            
              Created
              February 22, 2024 20:49
            
              
                CentOS 9, disable auto updates
              
          
    The updating comes from a package manager that is automatically enabled.
To stop from updating you need to stop the service with the following:
systemctl stop packagekit.service

  
## build_measures_csv.py
import os
import pandas as pd
import argparse
from tqdm import tqdm

def read_cluster_mapping(cluster_mapping_file, hemisphere_code):
    """Read cluster mapping file and return clusters for the specified hemisphere code ('l', 'r', 'c')."""
    cluster_df = pd.read_csv(cluster_mapping_file)
    relevant_clusters = cluster_df[cluster_df['Location_Label'] == hemisphere_code]['Cluster_Index'].tolist()
    return relevant_clusters

## extract_dicom_metadata.py
#!/usr/bin/env python3
import os
import csv
import argparse
import re
from tqdm import tqdm
from pydicom.filereader import dcmread
from pydicom.errors import InvalidDicomError
from pydicom.datadict import dictionary_keyword

## rebuild_icon_cache.bat
@echo off
SETLOCAL

echo This script will attempt to fix your icon cache.
echo Please save all work as your Windows Explorer will be restarted.
echo Press any key to continue...
pause > nul

echo.
echo Killing Explorer process...

## dice_calculator.py
#!/usr/bin/env python3
import numpy
import nibabel
import argparse


def calculate_dice_coefficients(file1, file2):
    input1_nii = nibabel.load(file1)
    input2_nii = nibabel.load(file2)

## process_transformations.py
#!/usr/bin/env python3
import os
import subprocess
import argparse
from tqdm import tqdm
from multiprocessing import Pool


def format_filename(filename):
    """

## process_wm_data.py
#!/usr/bin/env python3

import os
import subprocess
import argparse
import shlex
from multiprocessing import Pool


def process_file(args):

## chimera_setup_v2.md

      
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                RyanZurrin
                / chimera_setup_v2.md
            
            
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              November 21, 2023 16:00
            
              
                quick and easy to follow guide to set up chimera env
              
          
connect to chimera


2 hop from umb unix:
ssh -tt username@users3.cs.umb.edu ssh -tt username@chimera.umb.edu


2 hop from lab machine (gonzo, gargoyle, vampire)
ssh -tt username@lab_computer.verymad.net ssh -tt username@chimera.umb.edu


1 hop from lab machine:
ssh -tt username@chimera.umb.edu


## create_softlinks.sh
#!/bin/bash

# Initialize variables
root_dir=""
session=""
directions=""

# Parse command line arguments
while getopts "r:s:d:" opt; do
  case $opt in

## replace_substrings.py
import os
import glob
import argparse
from tqdm import tqdm


def rename_files_in_dir(target_dir, search_str, replace_str):
    renamed_files = []
    # Use glob to get all filenames that contain the specified search string
    filenames = glob.glob(f"{target_dir}/*{search_str}*")
	import os
	import pandas as pd
	import argparse
	from tqdm import tqdm

	def read_cluster_mapping(cluster_mapping_file, hemisphere_code):
	"""Read cluster mapping file and return clusters for the specified hemisphere code ('l', 'r', 'c')."""
	cluster_df = pd.read_csv(cluster_mapping_file)
	relevant_clusters = cluster_df[cluster_df['Location_Label'] == hemisphere_code]['Cluster_Index'].tolist()
	return relevant_clusters
	#!/usr/bin/env python3
	import os
	import csv
	import argparse
	import re
	from tqdm import tqdm
	from pydicom.filereader import dcmread
	from pydicom.errors import InvalidDicomError
	from pydicom.datadict import dictionary_keyword
	@echo off
	SETLOCAL

	echo This script will attempt to fix your icon cache.
	echo Please save all work as your Windows Explorer will be restarted.
	echo Press any key to continue...
	pause > nul

	echo.
	echo Killing Explorer process...
	#!/usr/bin/env python3
	import numpy
	import nibabel
	import argparse


	def calculate_dice_coefficients(file1, file2):
	input1_nii = nibabel.load(file1)
	input2_nii = nibabel.load(file2)
	#!/usr/bin/env python3
	import os
	import subprocess
	import argparse
	from tqdm import tqdm
	from multiprocessing import Pool


	def format_filename(filename):
	"""
	#!/bin/bash

	# Initialize variables
	root_dir=""
	session=""
	directions=""

	# Parse command line arguments
	while getopts "r:s:d:" opt; do
	case $opt in
	import os
	import glob
	import argparse
	from tqdm import tqdm


	def rename_files_in_dir(target_dir, search_str, replace_str):
	renamed_files = []
	# Use glob to get all filenames that contain the specified search string
	filenames = glob.glob(f"{target_dir}/{search_str}")