if (($file = fopen($csvFile , "r")) != FALSE) {
        $ctr = 0;
        $record = fgetcsv($file, 1024)) != FALSE) {
            if ($ctr == 0) {
                correctHeader($record);
                # write to new csv.
            } else {
                # write to new csv.
            }
        }
    }

<?php
$from = 'd.csv';
$to = 'd.good.csv';

$old = fopen($from, 'r');
if (!is_resource($old)) {
    die("Failed to read from source file: $from");
}

$headerLine = fgets($old);
$headerLine = fixHeaders($headerLine);

$new = fopen($to, 'w');
if (!is_resource($new)) {
    die("Failed to write to destination file: $new");
}
// Save the fixed header into the new file
fputs($new, $headerLine);
// Read the rest of old and save to new.
// Old file is already open and we are the second line.
// For large files, reading should probably be done in the loop with chunks.
fwrite($new, fread($old, filesize($from)));

// Close files
fclose($old);
fclose($new);

// Just an example
function fixHeaders($line) {
    return strtoupper($line);
}