A wrapper to allow Freesurfer's mri_convert to work on a tarball of dicoms.

convert_tarred_dicoms

#!/bin/bash

in_file="$1"
out_file="$2"

out_base=$(dirname "${out_file}")

tmp_dir=$(mktemp -d -p "${out_base}")
if [ $? -ne 0 ]; then
    echo "Can't make a temporary directory in ${out_base}" >&2
    exit 1
fi

echo -n "Untarring ${in_file} to ${tmp_dir}"
tar -C "${tmp_dir}" -xf "${in_file}" --checkpoint=.100
if [ $? -ne 0 ]; then
    echo
    echo "Error untarring ${in_file}" >&2
    rmdir "${tmp_dir}"
    exit 2
fi

echo
echo "Converting..."
# This will find you the first file...
first_file=$(find "${tmp_dir}" -type f | sed 1q)
mri_convert "${first_file}" "${out_file}"

'rm' -r "${tmp_dir}"

@njvack: would tarfile + pydicom + dcmstack let you do this with untarring?

I tried dcmstack; it was too slow for my purposes. mri_convert handles an 8400-slice EPI series in less than a minute; I gave up after waiting an hour for dcmstack to do its tricks.

It's a pity, because I really would like to annotate the niftis with the dicom headers.