#!/bin/bash

subjs=(pial_edits_before \
pial_edits_after \
wm1_edits_before \ 
wm1_edits_after \
topo_defect_before \
topo_defect_after \
skullstrip1_before \
skullstrip1_after \
cp_before \
cp_after \
tal_before \
tal_after \
bert)

mri_files=(aparc+aseg.mgz \
aseg.mgz \
brain.finalsurfs.mgz \
brainmask.mgz \
norm.mgz \
orig.mgz \
T1.mgz \
wm.mgz)

transforms_files=(talairach.xfm \
talairach.lta)

label_files=(?h.aparc.annot \
?h.cortex.label)

surf_files=(?h.defect_labels \
?h.inflated \
?h.inflated.nofix \
?h.orig \
?h.orig.nofix \
?h.pial \
?h.white)

MASTER="/space/freesurfer/subjects/tutorial/buckner_data/tutorial_subjs"
LIGHT="/cluster/pubftp/data/tutorial_data/buckner_data/tutorial_subjs"

for subj in ${subjs[@]}; do
  for mri_file in ${mri_files[@]} ; do
    cmd="cp ${MASTER}/${subj}/mri/${mri_file} ${LIGHT}/${subj}/mri/"
    echo "${cmd}"
    ${cmd}
  done
  if [ ! -d ${MASTER}/${subj}/mri/transforms ] ; then
    cmd="mkdir ${MASTER}/${subj}/mri/transforms"
    echo "${cmd}"
    ${cmd}
  fi
  for transforms_file in ${transforms_files[@]} ; do
    cmd="cp ${MASTER}/${subj}/mri/transforms/${transforms_file} ${LIGHT}/${subj}/mri/transforms/"
    echo "${cmd}"
    ${cmd}
  done
  for label_file in ${label_files[@]} ; do
    cmd="cp ${MASTER}/${subj}/label/${label_file} ${LIGHT}/${subj}/label/"
    echo "${cmd}"
    ${cmd}
  done
  for surf_file in ${surf_files[@]} ; do
    cmd="cp ${MASTER}/${subj}/surf/${surf_file} ${LIGHT}/${subj}/surf/"
    echo "${cmd}"
    ${cmd}
  done
  if [ ! -d ${MASTER}/${subj}/tmp ] ; then
    cmd="mkdir ${MASTER}/${subj}/tmp"
    echo "${cmd}"
    ${cmd}
  fi

done