示例#1
0
def _singleframe_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert a philips singleframe series to a nifti
    """

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _singleframe_to_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine, slice_increment = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    if full_block.ndim > 3:  # do not squeeze single slice data
        full_block = full_block.squeeze()
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))

    if output_file is not None:
        # Save to disk
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.header.set_slope_inter(1, 0)
        nii_image.header.set_xyzt_units(
            2)  # set units for xyz (leave t as unknown)
        nii_image.to_filename(output_file)

    if _is_singleframe_diffusion_imaging(grouped_dicoms):
        bval_file = None
        bvec_file = None
        # Create the bval en bvec files
        if output_file is not None:
            base_name = os.path.splitext(output_file)[0]
            if base_name.endswith('.nii'):
                base_name = os.path.splitext(base_name)[0]

            logger.info('Creating bval en bvec files')
            bval_file = '%s.bval' % base_name
            bvec_file = '%s.bvec' % base_name
        nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(
            grouped_dicoms, bval_file, bvec_file, nii_image, output_file)

        return {
            'NII_FILE': output_file,
            'BVAL_FILE': bval_file,
            'BVEC_FILE': bvec_file,
            'NII': nii_image,
            'BVAL': bval,
            'BVEC': bvec,
            'MAX_SLICE_INCREMENT': slice_increment
        }

    return {
        'NII_FILE': output_file,
        'NII': nii_image,
        'MAX_SLICE_INCREMENT': slice_increment
    }
def _classic_4d_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert siemens 4d series to a nifti
    Some inspiration on which fields can be used was taken from
    http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
    """
    # Get the sorted mosaics
    all_dicoms = [i for sl in grouped_dicoms
                  for i in sl]  # combine into 1 list for validating
    common.validate_orientation(all_dicoms)

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _classic_get_full_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine, slice_increment = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))
    logger.info('Saving nifti to disk')
    # Save to disk
    if output_file is not None:
        nii_image.to_filename(output_file)

    if _is_diffusion_imaging(grouped_dicoms[0][0]):
        logger.info('Creating bval en bvec')
        bval_file = None
        bvec_file = None
        if output_file is not None:
            base_path = os.path.dirname(output_file)
            base_name = os.path.splitext(
                os.path.splitext(os.path.basename(output_file))[0])[0]
            logger.info('Creating bval en bvec files')
            bval_file = '%s/%s.bval' % (base_path, base_name)
            bvec_file = '%s/%s.bvec' % (base_path, base_name)

        bval = _create_bvals(grouped_dicoms, bval_file)
        bvec = _create_bvecs(grouped_dicoms, bvec_file)

        return {
            'NII_FILE': output_file,
            'BVAL_FILE': bval_file,
            'BVEC_FILE': bvec_file,
            'NII': nii_image,
            'BVAL': bval,
            'BVEC': bvec,
            'MAX_SLICE_INCREMENT': slice_increment
        }

    return {
        'NII_FILE': output_file,
        'NII': nii_image,
        'MAX_SLICE_INCREMENT': slice_increment
    }
def dicom_to_nifti(dicom_input, output_file):
    """
    This function will convert an anatomical dicom series to a nifti

    Examples: See unit test

    :param output_file: filepath to the output nifti
    :param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
    """
    if len(dicom_input) <= 0:
        raise ConversionError('NO_DICOM_FILES_FOUND')

    # remove duplicate slices based on position and data
    dicom_input = _remove_duplicate_slices(dicom_input)

    # remove localizers based on image type
    dicom_input = _remove_localizers_by_imagetype(dicom_input)
    if settings.validate_slicecount:
        # remove_localizers based on image orientation (only valid if slicecount is validated)
        dicom_input = _remove_localizers_by_orientation(dicom_input)

        # validate all the dicom files for correct orientations
        common.validate_slicecount(dicom_input)
    if settings.validate_orientation:
        # validate that all slices have the same orientation
        common.validate_orientation(dicom_input)
    if settings.validate_orthogonal:
        # validate that we have an orthogonal image (to detect gantry tilting etc)
        common.validate_orthogonal(dicom_input)

    # sort the dicoms
    dicom_input = common.sort_dicoms(dicom_input)

    if settings.validate_sliceincrement:
        # validate that all slices have a consistent slice increment
        common.validate_sliceincrement(dicom_input)

    # Get data; originally z,y,x, transposed to x,y,z
    data = common.get_volume_pixeldata(dicom_input)

    affine = common.create_affine(dicom_input)

    # Convert to nifti
    nii_image = nibabel.Nifti1Image(data, affine)

    # Set TR and TE if available
    if Tag(0x0018, 0x0081) in dicom_input[0] and Tag(0x0018,
                                                     0x0081) in dicom_input[0]:
        common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime),
                         float(dicom_input[0].EchoTime))

    # Save to disk
    if output_file is not None:
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.to_filename(output_file)

    return {'NII_FILE': output_file, 'NII': nii_image}
示例#4
0
def _singleframe_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert a philips singleframe series to a nifti
    """

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _singleframe_to_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine, slice_increment = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime), float(grouped_dicoms[0][0].EchoTime))

    if output_file is not None:
        # Save to disk
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.to_filename(output_file)

    if _is_singleframe_diffusion_imaging(grouped_dicoms):
        bval_file = None
        bvec_file = None
        # Create the bval en bvec files
        if output_file is not None:
            base_name = os.path.splitext(output_file)[0]
            if base_name.endswith('.nii'):
                base_name = os.path.splitext(base_name)[0]

            logger.info('Creating bval en bvec files')
            bval_file = '%s.bval' % base_name
            bvec_file = '%s.bvec' % base_name
        nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(grouped_dicoms,
                                                                                      bval_file,
                                                                                      bvec_file,
                                                                                      nii_image,
                                                                                      output_file)

        return {'NII_FILE': output_file,
                'BVAL_FILE': bval_file,
                'BVEC_FILE': bvec_file,
                'NII': nii_image,
                'BVAL': bval,
                'BVEC': bvec,
                'MAX_SLICE_INCREMENT': slice_increment}

    return {'NII_FILE': output_file,
            'NII': nii_image,
            'MAX_SLICE_INCREMENT': slice_increment}
示例#5
0
def _convert_slice_incement_inconsistencies(dicom_input):
    """
    If there is slice increment inconsistency detected, for the moment CT images, then split the volumes into subvolumes based on the slice increment and process each volume separately using a space constructed based on the highest resolution increment
    """

    #   Estimate the "first" slice increment based on the 2 first slices
    increment = numpy.array(dicom_input[0].ImagePositionPatient) - numpy.array(
        dicom_input[1].ImagePositionPatient)

    # Create as many volumes as many changes in slice increment. NB Increments might be repeated in different volumes
    max_slice_increment = 0
    slice_incement_groups = []
    current_group = [dicom_input[0], dicom_input[1]]
    previous_image_position = numpy.array(dicom_input[1].ImagePositionPatient)
    for dicom in dicom_input[2:]:
        current_image_position = numpy.array(dicom.ImagePositionPatient)
        current_increment = previous_image_position - current_image_position
        max_slice_increment = max(max_slice_increment,
                                  numpy.linalg.norm(current_increment))
        if numpy.allclose(increment, current_increment, rtol=0.05, atol=0.1):
            current_group.append(dicom)
        if not numpy.allclose(
                increment, current_increment, rtol=0.05, atol=0.1):
            slice_incement_groups.append(current_group)
            current_group = [current_group[-1], dicom]
            increment = current_increment
        previous_image_position = current_image_position
    slice_incement_groups.append(current_group)

    # Create nibabel objects for each volume based on the corresponding headers
    slice_incement_niftis = []
    slice_increments = []
    voxel_sizes = {}
    for dicom_slices in slice_incement_groups:
        data = common.get_volume_pixeldata(dicom_slices)
        affine, _ = common.create_affine(dicom_slices)
        current_volume = nibabel.Nifti1Image(data.squeeze(), affine)
        slice_increment = numpy.linalg.norm(current_volume.header.get_zooms())
        voxel_sizes['%.5f' %
                    slice_increment] = current_volume.header.get_zooms()
        slice_increments.extend([slice_increment] * (len(dicom_slices) - 1))
        slice_incement_niftis.append(current_volume)

    tenth_percentile_incement = numpy.percentile(slice_increments, 15)
    most_used_increment = min(slice_increments,
                              key=lambda x: abs(x - tenth_percentile_incement))
    voxel_size = voxel_sizes['%.5f' % most_used_increment]

    nifti_volume = resample.resample_nifti_images(slice_incement_niftis,
                                                  voxel_size=voxel_size)

    return nifti_volume, max_slice_increment
示例#6
0
def _classic_4d_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert siemens 4d series to a nifti
    Some inspiration on which fields can be used was taken from
    http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
    """
    # Get the sorted mosaics
    all_dicoms = [i for sl in grouped_dicoms for i in sl]  # combine into 1 list for validating
    common.validate_orientation(all_dicoms)

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _classic_get_full_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine, slice_increment = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime), float(grouped_dicoms[0][0].EchoTime))
    logger.info('Saving nifti to disk')
    # Save to disk
    if output_file is not None:
        nii_image.to_filename(output_file)

    if _is_diffusion_imaging(grouped_dicoms[0][0]):
        logger.info('Creating bval en bvec')
        bval_file = None
        bvec_file = None
        if output_file is not None:
            base_path = os.path.dirname(output_file)
            base_name = os.path.splitext(os.path.splitext(os.path.basename(output_file))[0])[0]
            logger.info('Creating bval en bvec files')
            bval_file = '%s/%s.bval' % (base_path, base_name)
            bvec_file = '%s/%s.bvec' % (base_path, base_name)

        bval = _create_bvals(grouped_dicoms, bval_file)
        bvec = _create_bvecs(grouped_dicoms, bvec_file)

        return {'NII_FILE': output_file,
                'BVAL_FILE': bval_file,
                'BVEC_FILE': bvec_file,
                'NII': nii_image,
                'BVAL': bval,
                'BVEC': bvec,
                'MAX_SLICE_INCREMENT': slice_increment}

    return {'NII_FILE': output_file,
            'NII': nii_image,
            'MAX_SLICE_INCREMENT': slice_increment}
示例#7
0
def _4d_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert ge 4d series to a nifti
    """

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _get_full_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine, slice_increment = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))
    logger.info('Saving nifti to disk %s' % output_file)
    # Save to disk
    if output_file is not None:
        nii_image.header.set_slope_inter(1, 0)
        nii_image.header.set_xyzt_units(
            2)  # set units for xyz (leave t as unknown)
        nii_image.to_filename(output_file)

    if _is_diffusion_imaging(grouped_dicoms):
        bval_file = None
        bvec_file = None
        # Create the bval en bevec files
        if output_file is not None:
            base_path = os.path.dirname(output_file)
            base_name = os.path.splitext(
                os.path.splitext(os.path.basename(output_file))[0])[0]

            logger.info('Creating bval en bvec files')
            bval_file = '%s/%s.bval' % (base_path, base_name)
            bvec_file = '%s/%s.bvec' % (base_path, base_name)
        bval, bvec = _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file)
        return {
            'NII_FILE': output_file,
            'BVAL_FILE': bval_file,
            'BVEC_FILE': bvec_file,
            'NII': nii_image,
            'BVAL': bval,
            'BVEC': bvec,
            'MAX_SLICE_INCREMENT': slice_increment
        }

    return {'NII_FILE': output_file, 'NII': nii_image}
示例#8
0
def _singleframe_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert a philips singleframe series to a nifti
    """

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _singleframe_to_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    nii_image = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(nii_image, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))

    if output_file is not None:
        # Save to disk
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.to_filename(output_file)

    if _is_singleframe_diffusion_imaging(grouped_dicoms):
        bval_file = None
        bvec_file = None
        # Create the bval en bvec files
        if output_file is not None:
            base_name = os.path.splitext(output_file)[0]
            if base_name.endswith('.nii'):
                base_name = os.path.splitext(base_name)[0]

            logger.info('Creating bval en bvec files')
            bval_file = '%s.bval' % base_name
            bvec_file = '%s.bvec' % base_name
        nii_image, bval, bvec, bval_file, bvec_file = _create_singleframe_bvals_bvecs(
            grouped_dicoms, bval_file, bvec_file, nii_image, output_file)

        return {
            'NII_FILE': output_file,
            'BVAL_FILE': bval_file,
            'BVEC_FILE': bvec_file,
            'NII': nii_image,
            'BVAL': bval,
            'BVEC': bvec
        }
    return {'NII_FILE': output_file, 'NII': nii_image}
示例#9
0
def _singleframe_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert a philips singleframe series to a nifti
    """

    # Create mosaic block
    print('Creating data block')
    full_block = _singleframe_to_block(grouped_dicoms)

    print('Creating affine')
    # Create the nifti header info
    affine = common.create_affine(grouped_dicoms[0])

    print('Creating nifti')
    # Convert to nifti
    img = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(img, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))

    print('Saving nifti to disk %s' % output_file)
    # Save to disk
    img.to_filename(output_file)

    if _is_singleframe_diffusion_imaging(grouped_dicoms):
        # Create the bval en bvec files
        base_name = os.path.splitext(output_file)[0]
        if base_name.endswith('.nii'):
            base_name = os.path.splitext(base_name)[0]

        print('Creating bval en bvec files')
        bval_file = '%s.bval' % base_name
        bvec_file = '%s.bvec' % base_name
        bval_file, bvec_file = _create_singleframe_bvals_bvecs(
            grouped_dicoms, bval_file, bvec_file, img, output_file)

        result = {'NII_FILE': output_file}
        if bval_file is not None:
            result['BVAL_FILE'] = bval_file
        if bvec_file is not None:
            result['BVEC_FILE'] = bvec_file
        return result

    return {'NII_FILE': output_file}
示例#10
0
def _4d_to_nifti(grouped_dicoms, output_file):
    """
    This function will convert ge 4d series to a nifti
    """

    # Create mosaic block
    logger.info('Creating data block')
    full_block = _get_full_block(grouped_dicoms)

    logger.info('Creating affine')
    # Create the nifti header info
    affine = common.create_affine(grouped_dicoms[0])

    logger.info('Creating nifti')
    # Convert to nifti
    img = nibabel.Nifti1Image(full_block, affine)
    common.set_tr_te(img, float(grouped_dicoms[0][0].RepetitionTime),
                     float(grouped_dicoms[0][0].EchoTime))
    logger.info('Saving nifti to disk %s' % output_file)
    # Save to disk
    img.to_filename(output_file)

    if _is_diffusion_imaging(grouped_dicoms):
        # Create the bval en bevec files
        base_path = os.path.dirname(output_file)
        base_name = os.path.splitext(
            os.path.splitext(os.path.basename(output_file))[0])[0]

        logger.info('Creating bval en bvec files')
        bval_file = '%s/%s.bval' % (base_path, base_name)
        bvec_file = '%s/%s.bvec' % (base_path, base_name)
        _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file)
        return {
            'NII_FILE': output_file,
            'BVAL_FILE': bval_file,
            'BVEC_FILE': bvec_file
        }

    return {'NII_FILE': output_file}
示例#11
0
def _convert_slice_incement_inconsistencies(dicom_input):
    """
    If there is slice increment inconsistency detected, for the moment CT images, then split the volumes into subvolumes based on the slice increment and process each volume separately using a space constructed based on the highest resolution increment
    """

    #   Estimate the "first" slice increment based on the 2 first slices
    increment = numpy.array(dicom_input[0].ImagePositionPatient) - numpy.array(dicom_input[1].ImagePositionPatient)

    # Create as many volumes as many changes in slice increment. NB Increments might be repeated in different volumes
    max_slice_increment = 0
    slice_incement_groups = []
    current_group = [dicom_input[0], dicom_input[1]]
    previous_image_position = numpy.array(dicom_input[1].ImagePositionPatient)
    for dicom in dicom_input[2:]:
        current_image_position = numpy.array(dicom.ImagePositionPatient)
        current_increment = previous_image_position - current_image_position
        max_slice_increment = max(max_slice_increment, numpy.linalg.norm(current_increment))
        if numpy.allclose(increment, current_increment, rtol=0.05, atol=0.1):
            current_group.append(dicom)
        if not numpy.allclose(increment, current_increment, rtol=0.05, atol=0.1):
            slice_incement_groups.append(current_group)
            current_group = [current_group[-1], dicom]
            increment = current_increment
        previous_image_position = current_image_position
    slice_incement_groups.append(current_group)

    # Create nibabel objects for each volume based on the corresponding headers
    slice_incement_niftis = []
    for dicom_slices in slice_incement_groups:
        data = common.get_volume_pixeldata(dicom_slices)
        affine, _ = common.create_affine(dicom_slices)
        slice_incement_niftis.append(nibabel.Nifti1Image(data, affine))

    nifti_volume = resample.resample_nifti_images(slice_incement_niftis)

    return nifti_volume, max_slice_increment
示例#12
0
def dicom_to_nifti(dicom_input, output_file):
    """
    This function will convert an anatomical dicom series to a nifti

    Examples: See unit test

    :param output_file: filepath to the output nifti
    :param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
    """
    if len(dicom_input) <= 0:
        raise ConversionError('NO_DICOM_FILES_FOUND')

    # remove duplicate slices based on position and data
    dicom_input = remove_duplicate_slices(dicom_input)

    # remove localizers based on image type
    dicom_input = remove_localizers_by_imagetype(dicom_input)
    # if no dicoms remain we should raise exception
    if len(dicom_input) < 1:
        raise ConversionValidationError('TOO_FEW_SLICES/LOCALIZER')

    if settings.validate_slicecount:
        common.validate_slicecount(dicom_input)
        # remove_localizers based on image orientation (only valid if slicecount is validated)
        dicom_input = remove_localizers_by_orientation(dicom_input)

        # validate all the dicom files for correct orientations
        common.validate_slicecount(dicom_input)
    if settings.validate_orientation:
        # validate that all slices have the same orientation
        common.validate_orientation(dicom_input)
    if settings.validate_orthogonal:
        # validate that we have an orthogonal image (to detect gantry tilting etc)
        common.validate_orthogonal(dicom_input)

    # sort the dicoms
    dicom_input = common.sort_dicoms(dicom_input)

    # validate slice increment inconsistent
    slice_increment_inconsistent = False
    if settings.validate_slice_increment:
        # validate that all slices have a consistent slice increment
        common.validate_slice_increment(dicom_input)
    elif common.is_slice_increment_inconsistent(dicom_input):
        slice_increment_inconsistent = True

    if settings.validate_instance_number:
        # validate that all slices have a consistent instance_number
        common.validate_instance_number(dicom_input)


    # if inconsistent increment and we allow resampling then do the resampling based conversion to maintain the correct geometric shape
    if slice_increment_inconsistent and settings.resample:
        nii_image, max_slice_increment = _convert_slice_incement_inconsistencies(dicom_input)
    # do the normal conversion
    else:
        # Get data; originally z,y,x, transposed to x,y,z
        data = common.get_volume_pixeldata(dicom_input)

        affine, max_slice_increment = common.create_affine(dicom_input)

        # Convert to nifti
        nii_image = nibabel.Nifti1Image(data.squeeze(), affine)

    # Set TR and TE if available
    if Tag(0x0018, 0x0080) in dicom_input[0] and Tag(0x0018, 0x0081) in dicom_input[0]:
        common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime), float(dicom_input[0].EchoTime))

    # Save to disk
    if output_file is not None:
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.header.set_slope_inter(1, 0)
        nii_image.header.set_xyzt_units(2)  # set units for xyz (leave t as unknown)
        nii_image.to_filename(output_file)

    return {'NII_FILE': output_file,
            'NII': nii_image,
            'MAX_SLICE_INCREMENT': max_slice_increment}
示例#13
0
def dicom_to_nifti(dicom_input, output_file):
    """
    This function will convert an anatomical dicom series to a nifti

    Examples: See unit test

    :param output_file: filepath to the output nifti
    :param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
    """
    if len(dicom_input) <= 0:
        raise ConversionError('NO_DICOM_FILES_FOUND')

    # remove duplicate slices based on position and data
    dicom_input = _remove_duplicate_slices(dicom_input)

    # remove localizers based on image type
    dicom_input = _remove_localizers_by_imagetype(dicom_input)
    if settings.validate_slicecount:
        # remove_localizers based on image orientation (only valid if slicecount is validated)
        dicom_input = _remove_localizers_by_orientation(dicom_input)

        # validate all the dicom files for correct orientations
        common.validate_slicecount(dicom_input)
    if settings.validate_orientation:
        # validate that all slices have the same orientation
        common.validate_orientation(dicom_input)
    if settings.validate_orthogonal:
        # validate that we have an orthogonal image (to detect gantry tilting etc)
        common.validate_orthogonal(dicom_input)

    # sort the dicoms
    dicom_input = common.sort_dicoms(dicom_input)

    # validate slice increment inconsistent
    slice_increment_inconsistent = False
    if settings.validate_slice_increment:
        # validate that all slices have a consistent slice increment
        common.validate_slice_increment(dicom_input)
    elif common.is_slice_increment_inconsistent(dicom_input):
        slice_increment_inconsistent = True

    # if inconsistent increment and we allow resampling then do the resampling based conversion to maintain the correct geometric shape
    if slice_increment_inconsistent and settings.resample:
        nii_image, max_slice_increment = _convert_slice_incement_inconsistencies(dicom_input)
    # do the normal conversion
    else:
        # Get data; originally z,y,x, transposed to x,y,z
        data = common.get_volume_pixeldata(dicom_input)

        affine, max_slice_increment = common.create_affine(dicom_input)

        # Convert to nifti
        nii_image = nibabel.Nifti1Image(data, affine)

    # Set TR and TE if available
    if Tag(0x0018, 0x0081) in dicom_input[0] and Tag(0x0018, 0x0081) in dicom_input[0]:
        common.set_tr_te(nii_image, float(dicom_input[0].RepetitionTime), float(dicom_input[0].EchoTime))

    # Save to disk
    if output_file is not None:
        logger.info('Saving nifti to disk %s' % output_file)
        nii_image.to_filename(output_file)

    return {'NII_FILE': output_file,
            'NII': nii_image,
            'MAX_SLICE_INCREMENT': max_slice_increment}