Ryan Zurrin RyanZurrin

## feed-answer-notes.md

      
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                RyanZurrin
                / feed-answer-notes.md
            
            
              Created
              March 20, 2025 18:06
            
          
    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-


## libstdc_issue_fix.md

      
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                RyanZurrin
                / libstdc_issue_fix.md
            
            
              Created
              October 24, 2024 20:00
            
              
                Fix issue with libstdc++.so.6 which does not provide the required ABI version (CXXABI_1.3.9) as needed by some python packages (matplotlib and pillow).
              
          
    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

  
## local_tmux.md

      
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                RyanZurrin
                / local_tmux.md
            
            
              Last active
              October 25, 2024 13:40
            
          
    BUILDING TMUX LOCALLY
Set HOME directory: export HOME=/data/pnlx/home/$USER
Install OpenSSL

  
## renameToBIDSAnySession.sh
#!/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

## copy_random_subjects.sh
#!/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

## consolidate_csv_vtp_measures.py
import os
import pandas as pd
import glob
import argparse
from tqdm import tqdm

DEBUG = True
error_log = []
log = []

## space_usage_report.sh
#!/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

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

## dice_coefficient.py
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

## symlink_full_directory.sh
#!/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"
	#!/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
	#!/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
	import os
	import pandas as pd
	import glob
	import argparse
	from tqdm import tqdm

	DEBUG = True
	error_log = []
	log = []
	#!/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
	set number
	syntax on
	filetype plugin on
	set autoindent
	set smartindent
	set tabstop=4
	set shiftwidth=4
	set expandtab
	set wrap
	set showcmd
	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
	#!/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"