<commit_before>{
  "name": "dcm2niix",
  "label": "DCM2NIIX: v1.0.20170818",
  "description": "Chris Rorden's dcm2niiX version v1.0.20170818 (OpenJPEG build) GCC4.8.4 (64-bit Linux). dcm2niix is a popular tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the simple NIfTI format used by many scientific tools. dcm2niix works for all modalities (CT, MRI, PET, SPECT) and sequence types.",
  "maintainer": "<NAME> <<EMAIL>>",
  "author": "<NAME> (@neurolabusc)",
  "url": "https://github.com/rordenlab/dcm2niix",
  "source": "https://github.com/scitran-apps/dcm2niix",
  "license": "BSD-2-Clause",
  "flywheel": "0",
  "version": "0.2",
  "config": {
    "decompress_dicoms": {
      "default": false,
      "type": "boolean",
      "description": "Decompress DICOM files prior to conversion. This will perform decompression using gdcmconv and then perform conversion using dcm2niix. (true/false, default=false)"
    },
    "bids_sidecar": {
      "description": "Output BIDS sidecar in JSON format. (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-b"
    },
    "merge2d": {
      "description": "merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-m"
    },
    "text_notes_private": {
      "description": "text notes includes private patient details (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-t"
    },
    "crop": {
      "description": "Crop images (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-x"
    },
    "compress_nifti": {
      "description": "Compress output NIfTI file. Options, y=pigz, i=internal, n=no. (y/i/n, default=y) ",
      "type": "string",
      "default": "y",
      "id": "-z"
    },
    "filename": {
      "description": "Determine how files are named: filename (%a=antenna (coil) number, %c=comments, %d=description, %e=echo number, %f=folder name, %i=ID of patient, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %z=sequence name; [default='%f'])",
      "type": "string",
      "default": "%f",
      "id": "-f"
    },
    "anonymize_bids": {
      "description": "Anonymize BIDS (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-ba"
    },
    "ignore_derived": {
      "description": "ignore derived, localizer and 2D images (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-i"
    },
    "philips_scaling": {
      "description": "Philips precise float (not display) scaling (y/n, default y)",
      "type": "string",
      "default": "y",
      "id": "-p"
    },
    "single_file_mode": {
      "description": "single file mode, do not convert other images in folder (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-s"
    }
  },
  "inputs": {
    "dcm2niix_input": {
      "description": "Input file for dcm2niix. This can be either a DICOM archive ('.dicom.zip'), an enhanced DICOM file (gzipped or not, e.g., 'IM0001.gz', 'IM0001'), or a PAR/REC archive ('.parrec.zip')",
      "base": "file",
      "type": {
        "enum": [
          "dicom",
          "parrec"
        ]
      }
    }
  },
  "custom": {
    "docker-image": "scitran/dcm2niix:v0.2"
  }
}<commit_msg>dcm2niix-v0.2.1<commit_after>{
  "name": "dcm2niix",
  "label": "DCM2NIIX: v1.0.20170821",
  "description": "Chris Rorden's dcm2niiX version v1.0.20170821 (OpenJPEG build) GCC4.8.4 (64-bit Linux). dcm2niix is a popular tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the simple NIfTI format used by many scientific tools. dcm2niix works for all modalities (CT, MRI, PET, SPECT) and sequence types.",
  "maintainer": "<NAME> <<EMAIL>>",
  "author": "<NAME> (@neurolabusc)",
  "url": "https://github.com/rordenlab/dcm2niix",
  "source": "https://github.com/scitran-apps/dcm2niix",
  "license": "BSD-2-Clause",
  "flywheel": "0",
  "version": "0.2.1",
  "config": {
    "decompress_dicoms": {
      "default": false,
      "type": "boolean",
      "description": "Decompress DICOM files prior to conversion. This will perform decompression using gdcmconv and then perform conversion using dcm2niix. (true/false, default=false)"
    },
    "bids_sidecar": {
      "description": "Output BIDS sidecar in JSON format. (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-b"
    },
    "merge2d": {
      "description": "merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-m"
    },
    "text_notes_private": {
      "description": "text notes includes private patient details (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-t"
    },
    "crop": {
      "description": "Crop images (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-x"
    },
    "compress_nifti": {
      "description": "Compress output NIfTI file (y/n/3, default y)  [y=pigz, n=no, 3=no,3D]. Note that if option '3' is chosen, the filename flag will be set to '-f %p_%s' to prevent overwriting files",
      "type": "string",
      "default": "y",
      "id": "-z"
    },
    "filename": {
      "description": "Determine how files are named: filename (%a=antenna (coil) number, %c=comments, %d=description, %e=echo number, %f=folder name, %i=ID of patient, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %z=sequence name; [default='%f'])",
      "type": "string",
      "default": "%f",
      "id": "-f"
    },
    "anonymize_bids": {
      "description": "Anonymize BIDS (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-ba"
    },
    "ignore_derived": {
      "description": "ignore derived, localizer and 2D images (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-i"
    },
    "philips_scaling": {
      "description": "Philips precise float (not display) scaling (y/n, default y)",
      "type": "string",
      "default": "y",
      "id": "-p"
    },
    "single_file_mode": {
      "description": "single file mode, do not convert other images in folder (y/n, default n)",
      "type": "string",
      "default": "n",
      "id": "-s"
    },
    "3Dvol": {
      "description": "Output 3D uncompressed volumes (true/false, default=false). Note that the filename flag will be set to '-f %p_%s' to prevent overwriting files",
      "type": "boolean",
      "default": false
    }
  },
  "inputs": {
    "dcm2niix_input": {
      "description": "Input file for dcm2niix. This can be either a DICOM archive ('.dicom.zip'), an enhanced DICOM file (gzipped or not, e.g., 'IM0001.gz', 'IM0001'), or a PAR/REC archive ('.parrec.zip')",
      "base": "file",
      "type": {
        "enum": [
          "dicom",
          "parrec"
        ]
      }
    }
  },
  "custom": {
    "docker-image": "scitran/dcm2niix:v0.2.1"
  }
}
{'fraction_non_alphanumeric': 0.18370473537604456, 'fraction_numerical': 0.016434540389972146, 'mean_word_length': 2.873247033441208, 'pattern_counts': {'":': 150, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5419991', 'n_tokens_mistral': 2587, 'n_tokens_neox': 2510, 'n_words': 719}