usage: -input ilist flg arg varb arg2 dt Assign code values to each image (or specify a response template).

This option allows you to specify the timing of an fMRI task, or any other reference time course. The option is slightly complicated because it allows the timing information to be specified in many different ways. If you have a simple block designed task or event related task with fixed timing you may find it easier to use the -reference options to specify the reference time course. Alternatively, the -input option can be used to specify any reference time course by assigning a reference code value to each image in the functional imaging time series. The arguments to the -input option (as well as flags in the files pointed to by this option) allow you to control exactly how these image codes are generated.

Image codes can be specified explicitly as numbers, or as code words that are automatically converted into code numbers (first word in list is assigned code 1, and so on). In addition, code values can be assigned based on interpolating or extrapolating values from specified reference times (such as block transitions or interval start times). The nature of the image list and the format of the list itself can be specified by command line arguments (see FLAG below). If the input ILIST is a file (or text record) the first line of ILIST can affect the default settings of the FLAG argument (see FLAG below). Specifically, the words “events”, “template”, “blocks”, “transitions”, “images”, “starts”, “cycles”, “code”, “slice”, “volume”, “time”, and “duration” can be used to specify the format flags as indicated in parentheses in the FLAG options list. The FLAG ordering options (0100, 0200, 01000) can also be set based on the order of the relevant keywords in the first line of ILIST For backward compatibility, the keyword “stimrecfile” can also be used in place of “blocks” or “transitions”. Except for these keywords in the first line of ILIST, or code words in the code field of the data, any non-numeric text in the image list is treated as a comment flag, in which case the remainder of that line is ignored.

Image list option arguments can be specified as:

• ILIST - file name, or pdigm rec type or rec num for image index list. If ILIST is a floating pt. num. and FLAG has the 1, 2, or 3 bits then ILIST is the cycle/event interval (in secs).
• FLAG - this argument controls the meaning of timing information specified in ILIST. The default FLAG is 0, but this can be changed by the presence of keywords on the first line of the ILIST file (FLAG values set by keywords are indicated by the quoted keywords in the list above). The FLAG options are as follows (values are octal, combine by addition):
  • 0o - task codes are specified explicitly
  • 1o - task transitions are specified (“transitions” or “blocks”)
  • 2o - task start times are specified (“start”, code is time after start)
  • 3o - task cycle starts are specified (“cycle”, code is % of cycle)
  • 4o - response template is specified (“template”)
  • 010o - image numbers specified (“image”); otherwise assume times (“event”)
  • 020o - don't sort output by code value (usually sorted?)
  • 040o - duration of event is specified (“duration”)
  • 0100o - code in first column; otherwise code is last column
  • 0200o - volumns specified before slices (if 3 col input); else slice first
  • 0400o - numbering starts with 1; otherwise numbers start with 0
  • 01000o - list is in 3 columns (output: code, slicenum, and volnum)
  • 02000o - only code values are specified (image numbers are implicit)
  • 04000o - ignore code values (only used with “start” or “cycle”)
  • 010000o - save ilist as output file ILIST (will not overwrite existing file)
  • 020000o - input: values higher than max set to max, else ignored
  • 020000o - output: code values are in octal
  • 040000o - input: use explicit FLAG only (keywords ignored; otherwise added)
  • 040000o - output: 1 line per volume (volnum and codes for each slice)

Note: The default FLAG values for data order (100o, 200o, 1000o) will also be set automatically if possible, based on the order of the relevant keywords in the first line of ILIST. Some FLAG values can be specified by using one of the keywords on the command line instead of a numerical value. Those keywords and their number equivalents are listed below (these cannot be combined):

• blocks - 1
• starts - 2
• cycles - 3
• images - 8
• duration - 40o (input list format assumed to be either: time code length time length)
• template - 4

The meaning of the ARG and ARG2 arguments depends on the FLAG value: FLAG & 2 (STARTS)

• ARG is width of time bins (in secs) in which to code time after start. ARG2 is maximum number of time bins per event defaults: ARG is TR (1s if undefined); ARG2 is 0 (no maximum) FLAG & 3 (CYCLES) ARG is number of phase bins in which to divide each cycle. ARG2 is maximum time per cycle (in secs) defaults: ARG is 100; ARG2 is 0 (no maximum)
• VARB - reference variable to use for storing this image list. Up to 8 different reference lists can be specified (task1 - task8). The default VARB is the next available list ('taskX').
• DT - this parameter specifies how accurate to be about time values. DT is how close (in secs) two time values need to be to be considered equal. The default value is .02, which means that an event that occurs within 20 ms after an image is acquired is considered to be simultaneous with that image. This parameter helps avoid unexpected results due to small variabilities in timing values. To force maximum accuracy set DT to 0.

NOTES: Image numbering in image lists is based on XYZT order, not XYTZ. A negative condition code omits that image from processing. If the reference variable (VARB) is specified by name it can appear as the 2nd or 3rd argument (4th would be normal) in which case the missing FLAG and/or ARG argument values would be set to their default values.