Brain Finder Log File Format

This page details the format of a log file written using the Brain Finder tool, in Backus -Naur Form (BNF) notation. This is intended for those who wish to build their own syntactically correct parser to interpret these log files. A Brain Finder log entry is written by the Brain Finder tool as is a record of the calculation of the brain atrophy index.

A Brain Finder log file is a plain text file, consisting of a list (<bpf-entry-list>) of Brain Finder results. One result is generated each time a BPF is calculated and written to the log. In the Brain Finder log file, white space is used to separate the elements within an entry. White space may consist of space characters, tab characters or new-line characters. The amount of white space is not significant. Individual elements that may contain white space are enclosed in double quotes ("). Literal string elements are shown in non-italic font below.

<bpf-entry-list> ::= <bpf-spec>|<bpf-entry-list><bpf-spec>
<bpf-spec> ::=
Begin Entry
Brain Finder report produced by Jim 9.0
Build version=<version-spec>
BrainFinder report written on <date-time-spec> by Operator ID=<string-spec>
Image source=<string-spec>
<scan-spec>
Pixel width=<num-spec> mm
Pixel height=<num-spec> mm
Pixel depth=<num-spec> mm
<intensity-spec>
<auto-spec> CSF/brain threshold=<num-spec>
CSF volume=<num-spec> ml
Brain volume=<num-spec> ml
Brain+CSF volume=<num-spec> ml
BPF=<num-spec>
End Entry
<date-time-spec> ::= "dd mmm yyyy hh:mm:ss.SSS zzzz"
<intensity-spec> ::= CSF intensity=<num-spec>
Brain intensity=<num-spec>
|| <null>
<auto-spec> ::= "Automatic"|"User-defined"
<scan-spec> ::= defined here

<version-spec> is a string of ASCII text characters enclosed in double quotation marks (") giving the build version of Jim. The build version is of the form "MajorVersion_MinorVersion", e.g., "9.0_1"

<string-spec> is a string of ASCII text characters enclosed in double quotation marks (");

<num-spec> is a numerical value that may be either in integer or floating point format, depending on the context.

The CSF and brain and volumes are rounded to integer values. The BPF is written to an accuracy of four decimal places. If the user manually selected the intensity threshold, the intensity-spec not be present. If it is present, it shows Brain Finder's estimate of the CSF and brain peak positions in the intensity histogram. If separate peaks are fitted for the grey and white matter, then brain intensity shown is the intensity of the peak of lowest intensity.

Below is an example Brain Finder log entry for BPF calculated from an Analyze image "SPGR" in the directory "/home/xinapse". 

Begin Entry
  BrainFinder log written on "01 Dec 2020 14:19:41.876 GMT+00:00" by Operator ID="xinapse"
  Build version= "9.0_1"
  Image source= "/home/xinapse/SPGR.hdr"
  Pixel width=0.9375 mm
  Pixel height=0.9375 mm
  Pixel depth=1.5 mm
  CSF intensity=21
  Brain intensity=63
  Automatic CSF/brain threshold=42
  CSF volume=149934 ml
  Brain volume=1493195 ml
  Brain+CSF volume=1643129 ml
  BPF=0.9088
End Entry
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