DictionaryStructures.txt

# Fiff file structure dictionary
#
# Copyright (C) Megin Oy
#
# This is the complete dictionary.
# All rights reserved.
#
# $Log: DictionaryStructures.txt,v $
# Revision 1.8  2019/09/16 06:44:11  jne
# maxshield_record -> ias_record
# MAXSHIELD_RECORD -> IAS_RECORD
# maxshield -> ias
# raw_maxshield -> raw_ias
# maxshield_raw_data -> ias_raw_data
# evoked_maxshield -> evoked_ias
# maxshield_aspect -> ias_aspect
#
# Revision 1.7  2019/05/20 09:24:36  skesti
# Fixed ISOTRAK (extra '?'), raw_single and raw_multiple_1/2/n (extra '}')
#
# Revision 1.6  2019/05/14 07:33:23  skesti
# Added orig_file_guid, DEVICE_INFO, HELIUM_INFO, utc_offset.
#
# Revision 1.5  2018/07/02 05:27:10  jne
# Revision 1.4
#
# Revision 1.4  2011/05/06 08:29:05  janne
# Checking in earlier updates.
#
# Revision 1.3  2010/04/21 10:44:15  janne
# Updates to make Framemaker file proper.
#
# Revision 1.2  2010/04/20 13:19:14  janne
# Updated syntax definition.
#
# Revision 1.1  2010/04/20 11:46:34  janne
# Initial revision
#
#
#======================================================================

#======================================================================
#
# Syntax used in defining Fiff structures
#
# BLOCKS
#
# A block is described as a C-like block inside curly brackets. The type of the block
# is given as a variable name found in "DictionaryIOD.txt" before the starting
# bracket. The tags inside the block are indented once compared to the level of the
# block name.
#
# An example:
#
# block {
#	TAGS
# }
#
# TAGS
#
# Tags are given as variables defined in "DictionaryTags.txt". The data type of each
# tag is omitted. See "DictionaryTags.txt" for the data type and description of each
# tag. In general, no requirement is set for the ordering of tags inside a block.
#
# SEGMENT DEFINITIONS
#
# Below common segments are defined into separate variables in the following manner:
#
# SEGMENT =
#	tag
#	block {
#	      tag
#	}
#
# These segments can be used inside other segments:
#
# tag
# SEGMENT
# block {
#	tag
# }
#
# CONDITIONAL AND MULTIPLICATIVE STATEMENTS
#
# If the tag/block appears only once, and is required, it is written as it is:
#
# block {
#	tag
# }
#
# If the tag/block is required to appear n times in a row, a number is used inside
# square brackets:
#
# block[n] {
#	tag[n]
# }
#
# If the tag/block has to appear at least once, but can appear any number of times,
# use star symbol:
#
# block* {
#	tag
# }
#
# If the tag/block is conditional, use a question mark:
#
# block?{
#	tag?
# }
#
# Also multiplicative statements can be conditional. Place the question mark
# after the square brackets or the star symbol:
#
# block[n]? {
#	tag[n]?
# }
#
# block*? {
#	tag*?
# }
#
# If there are two interchangeable options for tag/block it is denoted by '|'
# between the options:
#
# block1 | block2 {
#	 tag1 | tag2
# }
#
#======================================================================

#======================================================================
#
# Common to blocks
#
#======================================================================
:id common_to_blocks
#======================================================================

<begin>
COMMON_TO_BLOCKS
	block {
	      block_id?
	      parent_block_id?
	}
<end>

#======================================================================
#
# Start of the file (common to all)
#
#======================================================================
:id file_start
#======================================================================

<begin>
FILE_START =
	file_id
	dir_pointer
	free_list?
	parent_file_id?
<end>

#======================================================================
#
# Subject information
#
#======================================================================
:id subject_info
#======================================================================

<begin>
SUBJECT_INFO =
	subject {
		subj_id
		subj_his_id?
		subj_last_name
		subj_first_name
		subj_middle_name?
		subj_birth_day?
		subj_sex?
		subj_hand?
		subj_weight?
		subj_height?
		subj_comment?
	}
<end>

#======================================================================
#
# Project information
#
#======================================================================
:id project_info
#======================================================================

<begin>
PROJECT_INFO =
	proj_id
	proj_name
	proj_comment?
<end>

#======================================================================
#
# Processing history
#
#======================================================================
:id processing_history
#======================================================================
<begin>
PROCESSING_HISTORY =
	processing_history? {
		PROCESSING_RECORD+
	}
<end>

#======================================================================
#
# Processing history
#
#======================================================================
:id processing_record
#======================================================================
<begin>
PROCESSING_RECORD =
	processing_record? {
		meas_date
		experimenter
		creator?
		PROCESSING_INFO+
	}
<end>

#======================================================================
#
# SSS processing record
#
#======================================================================
:id sss_record
#======================================================================

<begin>
SSS_RECORD =
	processing_record {
		meas_date
		experimenter
		creator
		sss_info {
			sss_job
			sss_frame
			sss_origin
			sss_ord_in
			sss_ord_out
			sss_nmag
			sss_components
			sss_nfree
		}
		channel_decoupler {
			meas_date
			creator
			decoupler_matrix
			sparse_ch_name_list
		}
		sss_cal_adjust {
			sss_cal_chans
			sss_cal_corrs
		}
	}
<end>

#======================================================================
#
# IAS processing record
#
#======================================================================
:id ias_record
#======================================================================

<begin>
IAS_RECORD =
	processing_record {
		meas_date
		experimenter
		ias {
		}
	}
<end>


#======================================================================
#
# Head position indicator (HPI) fitting results
#
#======================================================================
:id hpi_result
#======================================================================

<begin>
HPI_RESULT =
	hpi_result {
		dig_point*
		hpi_digitization_order
		hpi_coils_used
		hpi_coil_moments
		hpi_fit_goodness
		hpi_fit_good_limit
		hpi_fit_dist_limit
		hpi_fit_accept
		coord_trans			# device -> head
	}
<end>

#======================================================================
#
# Head position indicator (HPI) measurement
#
#======================================================================
:id hpi_meas
#======================================================================

<begin>
HPI_MEAS =
	hpi_meas {
		creator
		sfreq
		nchan
		nave
		hpi_ncoil
		first_sample
		last_sample
		hpi_coil+ {
			hpi_coil_no
			epoch+
			hpi_slopes
			hpi_corr_coeff
			hpi_coil_freq?
		}
	}
<end>

#======================================================================
#
# Isotrak digitized points and strings
#
#======================================================================
:id isotrak
#======================================================================

<begin>
ISOTRAK =
	isotrak {
		meas_date?
		dig_point+
		dig_string*
	}
<end>

#======================================================================
#
# Linear projection (SSP)
#
#======================================================================
:id ssp
#======================================================================

<begin>
SSP =
	ssp {
		nchan?
		proj_item+ {
			description
			proj_item_kind
			nchan?
			proj_item_ch_name_list
			proj_item_time
			proj_item_nvec
			proj_item_vectors
		}
	}
<end>

#======================================================================
#
# Device information
#
#======================================================================
:id device_info
#======================================================================

<begin>
DEVICE_INFO =
	device_info {
		device_type
		device_model?
		device_serial?
		device_site?
	}
<end>

#======================================================================
#
# Helium information
#
#======================================================================
:id helium_info
#======================================================================

<begin>
HELIUM_INFO =
	helium_info {
		he_level_raw?
		helium_level?
		gantry_angle?
		meas_date
	}
<end>

#======================================================================
#
# Measurement information
#
#======================================================================
:id meas_info
#======================================================================

<begin>
MEAS_INFO =
	meas_info {
		experimenter?
		description?
		orig_file_guid?
		events? {
			event_channels
			event_list
		}
		HPI_RESULT?
		HPI_MEAS?
		ISOTRAK?
		dacq_pars? {
			dacq_pars
			dacq_stim?
		}
		SUBJECT_INFO?
		PROJECT_INFO?
		SSP?
		DEVICE_INFO?
		HELIUM_INFO?
		meas_date
		utc_offset?
		nchan
		sfreq
		lowpass
		highpass
		line_freq?
		data_pack?
		gantry_angle?
		ch_info[nchan]
		bad_chs?
		hpi_subsystem? {
			hpi_ncoil
			event_channel
			hpi_coil+ {
				  event_bits
			}
		}
	}
<end>


#======================================================================
#
# Raw data in single file
#
#======================================================================
:id raw_single
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	PROCESSING_HISTORY?
	raw_data {
		first_samp?
		(data_buffer | data_skip | data_skip_samp)*
	}
}
nop
<end>

#======================================================================
#
# File reference block used in data splitted in multiple files
#
#======================================================================
:id file_reference
#======================================================================

<begin>
FILE_REFERENCE =
	ref {
	    ref_role
	    ref_file_id
	    ref_file_num
	}
<end>

#======================================================================
#
# Raw data in multiple files
#
#======================================================================
:id raw_multiple_1
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	raw_data {
		first_samp?
		(data_buffer | data_skip | data_skip_samp)*
		FILE_REFERENCE
	}
}
nop
<end>

#======================================================================
:id raw_multiple_2
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	raw_data {
		FILE_REFERENCE
		first_samp?
		(data_buffer | data_skip | data_skip_samp)*
		FILE_REFERENCE
	}
}
nop
<end>

#======================================================================
:id raw_multiple_n
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	raw_data {
		FILE_REFERENCE
		first_samp?
		(data_buffer | data_skip | data_skip_samp)*
	}
}
nop
<end>



#======================================================================
#
# Raw IAS data
#
#======================================================================
:id raw_ias
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	processing_history {
		IAS_RECORD
	}
	ias_raw_data {
		first_samp?
		(data_buffer | data_skip | data_skip_samp)*
	}
}
nop
<end>

#======================================================================
#
# Processed raw data
#
#======================================================================
:id processed_raw
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	PROCESSING_HISTORY
	processed_data {
		continuous_data {
			first_samp?
			(data_buffer | data_skip |
			data_skip_samp)*
		}
	}
}
nop
<end>

#======================================================================
#
# Evoked (averaged) data
#
#======================================================================
:id evoked_data
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	PROCESSING_HISTORY
	processed_data {
		evoked+ {
		       ref_event
		       first_sample
		       last_sample
		       event_comment?
		       comment?
		       aspect {
			      aspect_kind
			      nave?
			      epoch+
		       }
		}
	}
}
nop
<end>

#======================================================================
#
# Evoked IAS data
#
#======================================================================
:id evoked_ias
#======================================================================

<begin>
FILE_START
measurement {
	MEAS_INFO
	processing_history? {
		IAS_RECORD
	}
	processed_data {
		evoked+ {
		       ref_event
		       first_sample
		       last_sample
		       event_comment?
		       comment?
		       ias_aspect {
			      aspect_kind
			      nave?
			      epoch+
		       }
		}
	}
}
nop
<end>

#======================================================================
#
# Pixel data is included in the FIFF file
#
#======================================================================
:id pixel_data_included
#======================================================================

<begin>
PIXEL_DATA_INCLUDED =
	mri_pixel_data
	mri_pixel_type?			# Can be omitted only if mri_pixel_data's FIFF
					# data type matches with the actual data type
	mri_orig_source_path?
	mri_orig_source_format?
<end>

#
#======================================================================
#
# Pixel data is referenced from an external file:
#
#======================================================================
:id pixel_data_referenced
#======================================================================

<begin>
PIXEL_DATA_REF =
	ref_path
	mri_source_format
	mri_pixel_type
	mri_pixel_data_offset
<end>


#======================================================================
#
# Structural image (mri) data
#
#======================================================================
:id structural_data
#======================================================================

<begin>
FILE_START
structural_data {
	SUBJECT_INFO?
	PROCESSING_HISTORY?
	volume_data+ {
		coord_trans?		    # head -> MRI
		dig_point[3]?
		volume_slice+ {
			mri_width
			mri_width_m
			mri_height
			mri_height_m
			coord_trans         # MRI slice ->MRI
			PIXEL_DATA_INCLUDED | PIXEL_DATA_REF
			mri_pixel_scale
		}
	}
}
nop
<end>

#======================================================================
#
# Triangular BEM meshes
#
#======================================================================
:id bem
#======================================================================

<begin>
FILE_START
bem {
	SUBJECT_INFO?
	PROCESSING_HISTORY?
	bem_coord_frame
	coord_trans	             # head -> mri
	bem_surf+ {
		bem_surf_id
		bem_sigma
		bem_surf_nnode
		bem_surface_ntri
		bem_surface_nodes
		bem_surface_normals?
		bem_surface_triangles
	}
	bem_approx?
	bem_pot_solution?
}
nop
<end>

#======================================================================
#
# Screen captures
#
#======================================================================
:id scenery
#======================================================================

<begin>
FILE_START
scenery {
	SUBJECT_INFO?
	PROCESSING_HISTORY?
	coord_trans    # head -> MRI
	mri_scene_aim
	scene+ {
		mri_width
		mri_width_m
		mri_height
		mri_height_m
		coord_trans    # MRI slice -> MRI
		block_name
		mri_pixel_data
		mri_source_format
		mri_pixel_scale
	}
}
nop
<end>