RyanZurrin

Feed-Answer Unpacking and Processing Notes

1. Feed-Answer Unpacking

Identify the subjects you wish to unpack from DICOM to nifti format and create a case list text file of the subjects you wish to unpack. The case list text file should be formatted as follows:

sub-<subject_label>
sub-<subject_label>
sub-

RyanZurrin

Solution 1: Install GCC and libstdc++ via Conda

Create or Activate a Conda Environment If you don’t already have a Conda environment, create one:

conda create -n gcc_env python=3.8
conda activate gcc_env

RyanZurrin

BUILDING TMUX LOCALLY

Set HOME directory: export HOME=/data/pnlx/home/$USER

Install OpenSSL

RyanZurrin

#!/bin/bash

# Initialize variables
input_dir="/path/to/input/directory"
bids_root="/path/to/BIDS/rawdata/"
log_file="logs/$(date +%Y%m%d_%H%M%S)_renameToBIDSAnySession.log"
cases=""
case_list=""

# Function to display help message

RyanZurrin

#!/bin/bash

# Usage:
# ./copy_random_subjects.sh s3://nda-enclave-c3371/HCP/HCPD/ 10 /local/destination/path

S3_PATH="$1" # S3 bucket and path without trailing slash
NUM_SUBJECTS="$2" # Number of subjects to randomly select
DESTINATION_PATH="$3" # Local destination path

# Ensure awscli is installed

RyanZurrin

import os
import pandas as pd
import glob
import argparse
from tqdm import tqdm

DEBUG = True
error_log = []
log = []

RyanZurrin

#!/bin/bash

# Directory to scan; you can modify this to be the root '/' or any specific directory
TARGET_DIRECTORY="/"

# Output directory for the reports
REPORT_DIR="/var/log/space_reports"
mkdir -p "${REPORT_DIR}"

# Filename includes date for weekly tracking

RyanZurrin

set number
syntax on
filetype plugin on
set autoindent
set smartindent
set tabstop=4
set shiftwidth=4
set expandtab
set wrap
set showcmd

RyanZurrin

import nibabel as nib
import numpy as np
import csv
import sys
from tqdm import tqdm

def dice_coefficient(mask1, mask2):
    """
    Compute the Dice coefficient, a measure of set similarity.
    Parameters

RyanZurrin

#!/bin/bash

# Usage: ./symlink_full_dir.sh /path/to/source /path/to/target

SOURCE_DIR=$1
TARGET_DIR=$2

# Check if the source directory exists
if [ ! -d "$SOURCE_DIR" ]; then
    echo "Source directory does not exist: $SOURCE_DIR"