{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize subcortical pRF data for manuscript     \n",
    "First set up some paths and variables\n",
    "- Requires `fsl/fsleyes`\n",
    "- Rquires `NHP-pycortex` (https://github.com/VisionandCognition/NHP-pycortex)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ref_path=../../../FitResults/Reference\n",
    "res_path=../../../FitResults/MRI\n",
    "\n",
    "declare -a subs=(M01 M02)\n",
    "\n",
    "for SUBJ in ${subs[@]}; do\n",
    "    eval ${SUBJ}_t1=${ref_path}/Volumes/anat/${SUBJ}/sub-${SUBJ}_ref_anat_brain_res-0.5x0.5x0.5.nii.gz\n",
    "    eval ${SUBJ}_d99=${ref_path}/Volumes/atlas/${SUBJ}/D99_in_${SUBJ^}_adj.nii.gz\n",
    "    eval ${SUBJ}_roi_path=${ref_path}/Volumes/atlas/${SUBJ}/ROI_manualadjust/1mm\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Where to put output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "subcort_path=${res_path}/subcort\n",
    "mkdir -p ${subcort_path}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create some subcortical ROI masks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# cat rois\n",
    "for SUBJ in ${subs[@]}; do\n",
    "    eval fslmaths '$'${SUBJ}_roi_path/LGNm.nii.gz -add '$'${SUBJ}_roi_path/LGNp.nii.gz -bin ${subcort_path}/${SUBJ}_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_roi_path/PL.nii.gz -add '$'${SUBJ}_roi_path/PM.nii.gz -bin ${subcort_path}/${SUBJ}_PULV.nii.gz\n",
    "    eval fslmaths ${subcort_path}/${SUBJ}_PULV.nii.gz -add ${subcort_path}/${SUBJ}_LGN.nii.gz -bin ${subcort_path}/${SUBJ}_LGNPULV.nii.gz\n",
    "    eval cp '$'${SUBJ}_roi_path/Striatum.nii.gz ${subcort_path}/${SUBJ}_Striatum.nii.gz\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Which models / HRF / R2-threshold"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "model=csshrf\n",
    "hrf=mhrf\n",
    "RTH=3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show suprathreshold angles / eccentricity / size"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "M=${model}_cv1_${hrf}\n",
    "#M=${model}_cv1_${hrf}_neggain\n",
    "\n",
    "for SUBJ in ${subs[@]}; do\n",
    "    eval ${SUBJ}_R2=${res_path}/${SUBJ}/${M}/inAnat/Sess-${model}_cv1_${hrf}_meanR2.nii.gz\n",
    "    eval ${SUBJ}_ANG=${res_path}/${SUBJ}/${M}/inAnat/TH_$RTH/ANG_th${RTH}.nii.gz\n",
    "    eval ${SUBJ}_ECC=${res_path}/${SUBJ}/${M}/inAnat/TH_$RTH/ECC_th${RTH}.nii.gz\n",
    "    eval ${SUBJ}_X=${res_path}/${SUBJ}/${M}/inAnat/TH_$RTH/X_th${RTH}.nii.gz\n",
    "    eval ${SUBJ}_Y=${res_path}/${SUBJ}/${M}/inAnat/TH_$RTH/Y_th${RTH}.nii.gz\n",
    "    eval ${SUBJ}_RFS=${res_path}/${SUBJ}/${M}/inAnat/TH_$RTH/RFS_th${RTH}.nii.gz\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "P=${subcort_path}/${model}_${hrf}_${RTH}\n",
    "#P=${subcort_path}/${model}_neggain_${hrf}_${RTH}\n",
    "mkdir -p ${P}\n",
    "for SUBJ in ${subs[@]}; do\n",
    "    eval fslmaths '$'${SUBJ}_ANG -mas ${subcort_path}/${SUBJ}_LGN.nii.gz ${P}/${SUBJ}_ANG_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_ANG -mas ${subcort_path}/${SUBJ}_PULV.nii.gz ${P}/${SUBJ}_ANG_PULV.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_ANG -mas ${subcort_path}/${SUBJ}_Striatum.nii.gz ${P}/${SUBJ}_ANG_Striatum.nii.gz\n",
    "\n",
    "    eval fslmaths '$'${SUBJ}_ECC -mas ${subcort_path}/${SUBJ}_LGN.nii.gz ${P}/${SUBJ}_ECC_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_ECC -mas ${subcort_path}/${SUBJ}_PULV.nii.gz ${P}/${SUBJ}_ECC_PULV.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_ECC -mas ${subcort_path}/${SUBJ}_Striatum.nii.gz ${P}/${SUBJ}_ECC_Striatum.nii.gz\n",
    "    \n",
    "    eval fslmaths '$'${SUBJ}_X -mas ${subcort_path}/${SUBJ}_LGN.nii.gz ${P}/${SUBJ}_X_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_X -mas ${subcort_path}/${SUBJ}_PULV.nii.gz ${P}/${SUBJ}_X_PULV.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_X -mas ${subcort_path}/${SUBJ}_Striatum.nii.gz ${P}/${SUBJ}_X_Striatum.nii.gz\n",
    "\n",
    "    eval fslmaths '$'${SUBJ}_Y -mas ${subcort_path}/${SUBJ}_LGN.nii.gz ${P}/${SUBJ}_Y_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_Y -mas ${subcort_path}/${SUBJ}_PULV.nii.gz ${P}/${SUBJ}_Y_PULV.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_Y -mas ${subcort_path}/${SUBJ}_Striatum.nii.gz ${P}/${SUBJ}_Y_Striatum.nii.gz\n",
    "\n",
    "    eval fslmaths '$'${SUBJ}_RFS -mas ${subcort_path}/${SUBJ}_LGN.nii.gz ${P}/${SUBJ}_RFS_LGN.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_RFS -mas ${subcort_path}/${SUBJ}_PULV.nii.gz ${P}/${SUBJ}_RFS_PULV.nii.gz\n",
    "    eval fslmaths '$'${SUBJ}_RFS -mas ${subcort_path}/${SUBJ}_Striatum.nii.gz ${P}/${SUBJ}_RFS_Striatum.nii.gz\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# relies on fsleyes being installed\n",
    "for SUBJ in ${subs[@]}; do\n",
    "    M=${subcort_path}/${model}_${hrf}_${RTH}\n",
    "    P=${subcort_path}/${model}_${hrf}_${RTH}/${SUBJ}\n",
    "    eval 'fsleyes -no $'${SUBJ}_t1 \\\n",
    "        '$'${SUBJ}_R2 -dr 0 5 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_ANG_LGN.nii.gz -dr 0 360 -cm hsv \\\n",
    "        ${P}_ANG_PULV.nii.gz -dr 0 360 -cm hsv \\\n",
    "        ${P}_ANG_Striatum.nii.gz -dr 0 360 -cm hsv \\\n",
    "        ${P}_ECC_LGN.nii.gz -dr 0 10 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_ECC_PULV.nii.gz -dr 0 10 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_ECC_Striatum.nii.gz -dr 0 10 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_RFS_LGN.nii.gz -dr 0 4 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_RFS_PULV.nii.gz -dr 0 4 -cm brain_colours_5redyell_iso \\\n",
    "        ${P}_RFS_Striatum.nii.gz -dr 0 4 -cm brain_colours_5redyell_iso &       \n",
    "done\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Bash",
   "language": "bash",
   "name": "bash"
  },
  "language_info": {
   "codemirror_mode": "shell",
   "file_extension": ".sh",
   "mimetype": "text/x-sh",
   "name": "bash"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}