pycomsort.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "cb2ec4b2",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pydicom\n",
    "import os \n",
    "import glob\n",
    "import shutil"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "38cded37",
   "metadata": {},
   "outputs": [],
   "source": [
    "dicomfolder = \"/Users/kayti/Desktop/pycom_sort_test/dcm/\" \n",
    "niioutput = \"/Users/kayti/Desktop/pycom_sort_test/nii/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d320b6f5",
   "metadata": {},
   "outputs": [],
   "source": [
    "subjids = os.listdir(dicomfolder)\n",
    "if '.DS_Store' in subjids:\n",
    "  subjids.remove('.DS_Store')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "02dc2eed",
   "metadata": {},
   "outputs": [],
   "source": [
    "for ids in subjids:  \n",
    "  path = dicomfolder + ids + \"/**/*\"\n",
    "  dcmspath = glob.glob(path, recursive=True)\n",
    "  dcmspathfile = dcmspath[100]\n",
    "  dcmpath = os.path.dirname(dcmspathfile)\n",
    "  dcms = os.listdir(dcmpath)\n",
    "  if '.DS_Store' in dcms:\n",
    "      dcms.remove('.DS_Store')\n",
    "  for dcm in dcms:\n",
    "      dcmhdr = pydicom.dcmread(dcmpath + '/' + dcm)\n",
    "      pn = str(dcmhdr.ProtocolName)\n",
    "      sn = str(dcmhdr.SeriesNumber)\n",
    "      if os.path.exists(dicomfolder + '/' + ids + '/' + sn + '_' + pn):\n",
    "          oldfile = os.path.join(dcmpath + '/' + dcm)\n",
    "          newfile = os.path.join(dicomfolder + '/' + ids + '/' + sn +  '_' + pn + '/' + dcm)\n",
    "          os.rename(oldfile,newfile)\n",
    "      else: \n",
    "          os.mkdir(dicomfolder + '/' + ids + '/' + sn +  '_' + pn)\n",
    "          oldfile = os.path.join(dcmpath + '/' + dcm)\n",
    "          newfile = os.path.join(dicomfolder + '/' + ids + '/' + sn +  '_' + pn + '/' + dcm)\n",
    "          os.rename(oldfile,newfile)\n",
    "      for entry in os.scandir(dicomfolder + '/' + ids):\n",
    "        if os.path.isdir(entry.path) and not os.listdir(entry.path) :\n",
    "          os.rmdir(entry.path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0dae3e4e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dcm2niix -o /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b -f %p /Users/kayti/Desktop/pycom_sort_test/dcm/IAM_1127b\n",
      "Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0 (64-bit MacOS)\n",
      "Found 3003 DICOM file(s)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.0485872 0.950782 0.306028 -0.020759 0.307284 -0.951391] != [0.0449104 0.986194 0.159388 -0.0278335 0.160723 -0.986607]\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00003 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00004 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00002 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 240 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/t1_mprage_sag_p2_iso_MPR_Cor_i00001 (230x230x240x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 266 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 266 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/FBI_b8000_256_Siemens (74x74x42x266)\n",
      "Convert 62 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/t2_tse_dark-fluid_tra (256x256x62x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/sms3_3.0iso_Resting_State_2 (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/sms3_3.0iso_Resting_State_1 (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/sms3_3.0iso_Task (64x64x51x375)\n",
      "Convert 192 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/t1_mprage_sag_p2_iso (256x256x192x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998603 -0.0398726 -0.0346673 -0.0278335 0.160723 -0.986607] != [0.998808 -0.0374635 -0.031285 -0.024828 0.161869 -0.9865]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00002a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00001 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coila (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 250 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA (88x88x50x5)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 3 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/sms3_3.0iso_PA (64x64x51x3)\n",
      "slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/gre_field_mapping_e2 (64x64x51x1)\n",
      "slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/gre_field_mapping_e1 (64x64x51x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 70 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 70 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/DKI_MONOPOLAR_3.0mm_30dir_42slices_e1 (74x74x42x70)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 138 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 138 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/DKI_BIPOLAR_2.5mm_64dir_50slices (88x88x50x138)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 74 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 74 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/TDE_ep2d_diff_brad300_off (74x74x42x74)\n",
      "Convert 42 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/DKI_MONOPOLAR_3.0mm_30dir_42slices_topup (74x74x42x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998406 -0.0457172 -0.0330849 0.0504226 0.985959 0.159195] != [0.998603 -0.0398726 -0.0346673 0.0388075 0.99877 -0.0308718]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00001a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coil_i00002b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coilb (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 74 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 74 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/TDE_ep2d_diff_brad300 (74x74x42x74)\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/gre_field_mapping_e2_ph (64x64x51x1)\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/AAHead_Scout_32ch-head-coilc (160x160x128x1)\n",
      "Convert 175 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1127b/t1_mprage_sag_p2_iso_MPR_Tra (230x230x175x1)\n",
      "Conversion required 4.636918 seconds (4.619582 for core code).\n",
      "dcm2niix -o /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2 -f %p /Users/kayti/Desktop/pycom_sort_test/dcm/IAM_1128b2\n",
      "Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0 (64-bit MacOS)\n",
      "Found 2994 DICOM file(s)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [-0.59728 0.776161 0.202067 0.017468 0.264473 -0.964235] != [0.535427 0.811975 0.23241 0.017468 0.264473 -0.964235]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00004 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00002 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00001 (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00003 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 240 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/t1_mprage_sag_p2_iso_MPR_Cor_i00001 (230x230x240x1)\n",
      "Convert 62 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/t2_tse_dark-fluid_tra (256x256x62x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/sms3_3.0iso_Resting_State_2 (64x64x51x375)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998638 0.051881 0.00555224 0.000924887 0.0887932 -0.99605] != [0.996924 0.0433061 0.0653278 0.0610106 0.0944567 -0.993658]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00001a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00003a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/sms3_3.0iso_Resting_State_1 (64x64x51x375)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/sms3_3.0iso_Task (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 266 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 266 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/FBI_b8000_256_Siemens (74x74x42x266)\n",
      "Convert 192 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/t1_mprage_sag_p2_iso (256x256x192x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.996017 0.0354209 0.081826 0.0779029 0.100713 -0.991861] != [0.998965 0.041116 0.0194291 0.0153071 0.0982939 -0.99504]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00003b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00002a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coila (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coilb (160x160x128x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.533867 0.817819 0.214843 -0.00232524 0.2555 -0.966806] != [-0.0453611 0.973988 0.222014 -0.00865721 0.221851 -0.975042]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00002b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00001b (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00004a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coilc (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 250 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA (88x88x50x5)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 3 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/sms3_3.0iso_PA (64x64x51x3)\n",
      "slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/gre_field_mapping_e1 (64x64x51x1)\n",
      "slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/gre_field_mapping_e2 (64x64x51x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 138 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 138 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/DKI_BIPOLAR_2.5mm_64dir_50slices_e1 (88x88x50x138)\n",
      "Convert 42 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/DKI_MONOPOLAR_3.0mm_30dir_42slices_topup (74x74x42x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998983 0.0441361 0.0092613 -0.0450373 0.965801 0.255342] != [0.998933 0.046151 0.0016314 -0.0456337 0.99192 -0.118371]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00003c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00002c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coild (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998965 0.041116 0.0194291 -0.0387046 0.993021 -0.111404] != [0.996017 0.0354209 0.081826 -0.0433735 0.994285 0.0975521]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00002d (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coil_i00001c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coile (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/gre_field_mapping_e2_ph (64x64x51x1)\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/AAHead_Scout_32ch-head-coilf (160x160x128x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 70 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 70 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/DKI_MONOPOLAR_3.0mm_30dir_42slices (74x74x42x70)\n",
      "Convert 175 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b2/t1_mprage_sag_p2_iso_MPR_Tra (230x230x175x1)\n",
      "Conversion required 4.303893 seconds (4.295165 for core code).\n",
      "dcm2niix -o /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b -f %p /Users/kayti/Desktop/pycom_sort_test/dcm/IAM_1128b\n",
      "Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0 (64-bit MacOS)\n",
      "Found 2994 DICOM file(s)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [-0.59728 0.776161 0.202067 0.017468 0.264473 -0.964235] != [0.535427 0.811975 0.23241 0.017468 0.264473 -0.964235]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00004 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00002 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00001 (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00003 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 240 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/t1_mprage_sag_p2_iso_MPR_Cor_i00001 (230x230x240x1)\n",
      "Convert 62 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/t2_tse_dark-fluid_tra (256x256x62x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/sms3_3.0iso_Resting_State_2 (64x64x51x375)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998638 0.051881 0.00555224 0.000924887 0.0887932 -0.99605] != [0.996924 0.0433061 0.0653278 0.0610106 0.0944567 -0.993658]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00001a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00003a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/sms3_3.0iso_Resting_State_1 (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/sms3_3.0iso_Task (64x64x51x375)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 266 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 266 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/FBI_b8000_256_Siemens (74x74x42x266)\n",
      "Convert 192 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/t1_mprage_sag_p2_iso (256x256x192x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.996017 0.0354209 0.081826 0.0779029 0.100713 -0.991861] != [0.998965 0.041116 0.0194291 0.0153071 0.0982939 -0.99504]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00003b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00002a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coila (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coilb (160x160x128x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.533867 0.817819 0.214843 -0.00232524 0.2555 -0.966806] != [-0.0453611 0.973988 0.222014 -0.00865721 0.221851 -0.975042]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00002b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00001b (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00004a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coilc (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 250 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA (88x88x50x5)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 3 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/sms3_3.0iso_PA (64x64x51x3)\n",
      "slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/gre_field_mapping_e1 (64x64x51x1)\n",
      "slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/gre_field_mapping_e2 (64x64x51x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 138 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 138 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/DKI_BIPOLAR_2.5mm_64dir_50slices_e1 (88x88x50x138)\n",
      "Convert 42 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/DKI_MONOPOLAR_3.0mm_30dir_42slices_topup (74x74x42x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998983 0.0441361 0.0092613 -0.0450373 0.965801 0.255342] != [0.998933 0.046151 0.0016314 -0.0456337 0.99192 -0.118371]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00003c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00002c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coild (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998965 0.041116 0.0194291 -0.0387046 0.993021 -0.111404] != [0.996017 0.0354209 0.081826 -0.0433735 0.994285 0.0975521]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00002d (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coil_i00001c (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coile (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/gre_field_mapping_e2_ph (64x64x51x1)\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/AAHead_Scout_32ch-head-coilf (160x160x128x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 70 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 70 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/DKI_MONOPOLAR_3.0mm_30dir_42slices (74x74x42x70)\n",
      "Convert 175 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/IAM_1128b/t1_mprage_sag_p2_iso_MPR_Tra (230x230x175x1)\n",
      "Conversion required 4.260293 seconds (4.252791 for core code).\n",
      "dcm2niix -o /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b -f %p /Users/kayti/Desktop/pycom_sort_test/dcm/20220615_132131_IAM_1127b\n",
      "Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0 (64-bit MacOS)\n",
      "Found 3003 DICOM file(s)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.0485872 0.950782 0.306028 -0.020759 0.307284 -0.951391] != [0.0449104 0.986194 0.159388 -0.0278335 0.160723 -0.986607]\n",
      "Convert 2 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil (162x162x2x1)\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00003 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00004 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00002 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 240 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/t1_mprage_sag_p2_iso_MPR_Cor_i00001 (230x230x240x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 266 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 266 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/FBI_b8000_256_Siemens (74x74x42x266)\n",
      "Convert 62 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/t2_tse_dark-fluid_tra (256x256x62x1)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/sms3_3.0iso_Resting_State_2 (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/sms3_3.0iso_Resting_State_1 (64x64x51x375)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 375 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/sms3_3.0iso_Task (64x64x51x375)\n",
      "Convert 192 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/t1_mprage_sag_p2_iso (256x256x192x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998603 -0.0398726 -0.0346673 -0.0278335 0.160723 -0.986607] != [0.998808 -0.0374635 -0.031285 -0.024828 0.161869 -0.9865]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00002a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00001 (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coila (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 250 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA (88x88x50x5)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Convert 3 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/sms3_3.0iso_PA (64x64x51x3)\n",
      "slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/gre_field_mapping_e2 (64x64x51x1)\n",
      "slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/gre_field_mapping_e1 (64x64x51x1)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 70 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 70 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/DKI_MONOPOLAR_3.0mm_30dir_42slices_e1 (74x74x42x70)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 138 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 138 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/DKI_BIPOLAR_2.5mm_64dir_50slices (88x88x50x138)\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 74 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 74 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/TDE_ep2d_diff_brad300_off (74x74x42x74)\n",
      "Convert 42 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/DKI_MONOPOLAR_3.0mm_30dir_42slices_topup (74x74x42x1)\n",
      "slices not stacked: orientation varies (vNav or localizer?) [0.998406 -0.0457172 -0.0330849 0.0504226 0.985959 0.159195] != [0.998603 -0.0398726 -0.0346673 0.0388075 0.99877 -0.0308718]\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00001a (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coil_i00002b (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "Convert 1 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coilb (162x162x1x1)\n",
      "Warning: Check that 2D images are not mirrored.\n",
      "slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n",
      "Warning: Saving 74 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n",
      "Convert 74 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/TDE_ep2d_diff_brad300 (74x74x42x74)\n",
      "Convert 51 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/gre_field_mapping_e2_ph (64x64x51x1)\n",
      "Convert 128 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/AAHead_Scout_32ch-head-coilc (160x160x128x1)\n",
      "Convert 175 DICOM as /Users/kayti/Desktop/pycom_sort_test/nii/20220615_132131_IAM_1127b/t1_mprage_sag_p2_iso_MPR_Tra (230x230x175x1)\n",
      "Conversion required 4.547875 seconds (4.510929 for core code).\n"
     ]
    }
   ],
   "source": [
    "for ids in subjids:\n",
    "    dcm_folder = os.path.join(dicomfolder + ids)\n",
    "    output_folder = os.path.join(niioutput + ids)\n",
    "    cmd = os.path.join('dcm2niix -o ' + output_folder + ' -f %p ' + dcm_folder)\n",
    "    print(cmd)\n",
    "    if os.path.exists(output_folder):\n",
    "        os.system(cmd)\n",
    "    else: \n",
    "        os.mkdir(output_folder)\n",
    "        os.system(cmd)\n",
    "    \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "e1e4ed20",
   "metadata": {},
   "outputs": [],
   "source": [
    "#anat = [\"t1\", \"t2\"]\n",
    "orgdirs = [\"anat\", \"dwi\", \"fmap\", \"fmri\", \"others\"]\n",
    "for ids in subjids:\n",
    "    for od in orgdirs:\n",
    "        org_folder = output_folder + '/' + od\n",
    "        if os.path.exists(org_folder):\n",
    "            pass\n",
    "        else:\n",
    "          os.mkdir(org_folder)\n",
    "    output_folder = os.path.join(niioutput + ids)    \n",
    "    files = os.listdir(output_folder)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "87d640e4",
   "metadata": {},
   "outputs": [],
   "source": [
    "def copyCertainFiles(source_folder, dest_folder, string_to_match, file_type=None):\n",
    "    # Check all files in source_folder\n",
    "    for filename in os.listdir(source_folder):\n",
    "        # Move the file if the filename contains the string to match\n",
    "        if file_type == None:\n",
    "            if string_to_match in filename:\n",
    "                shutil.move(os.path.join(source_folder, filename), dest_folder)\n",
    "\n",
    "for ids in subjids:\n",
    "    nii_folder = niioutput + ids\n",
    "    anat = niioutput + ids + '/anat'  \n",
    "    dwi = niioutput + ids + '/dwi' \n",
    "    fmap = niioutput + ids + '/fmap' \n",
    "    fmri = niioutput + ids + '/fmri' \n",
    "    others = niioutput + ids + '/others' \n",
    "\n",
    "    copyCertainFiles(nii_folder, anat, \"t1\" , file_type=None)      \n",
    "    copyCertainFiles(nii_folder, anat, \"t2\" , file_type=None) \n",
    "    copyCertainFiles(nii_folder, others, \"AAHead\" , file_type=None) \n",
    "    copyCertainFiles(nii_folder, dwi, \"DKI\" , file_type=None) \n",
    "    copyCertainFiles(nii_folder, dwi, \"FBI\" , file_type=None)\n",
    "    copyCertainFiles(nii_folder, dwi, \"TDE\" , file_type=None)\n",
    "    copyCertainFiles(nii_folder, fmri, \"sms3\" , file_type=None)\n",
    "    copyCertainFiles(nii_folder, fmap, \"gre\" , file_type=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0c743ea0",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.7"
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 "nbformat": 4,
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