A volume list file (VLF) is an ASCII file containing information on a set of image files (volumes). The file has one line for each volume. Each line consists of a number of space separated fields that hold different bits of information about a volume. Optionally, at the top of a VLF there can exist Keyword/Value pairs which specify filename suffixes for the data and mask volumes. Comment lines in a VLF start with the '#' character. See the example below of a typical VLF.
Volume List File Fields:
The ordering of the fields in a VLF must be given as ordered in the list above.
This is an integer specifying the ordinal value within the volume list file. The first
volume has a volume number of 1, the second volume has a volume number of 2, etc.
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Filename of the data volume. The directory name is not included in the filename. Directory
names are added to the filename at a later time. This allows VLF's to be independent of where
the data lives. The filename suffix is also optional if the VOLSUFF
keyword is used. The value of this keyword is used as the filename suffix for all the data
volume files in the VLF (see example).
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Filename of the brain mask volume. The directory name is not included in the filename. Directory
names are added to the filename at a later time, allowing the VLF's to be independent of where
the data lives. The filename suffix is also optional if the MSKSUFF
keyword is used. The value of this keyword is used as the filename suffix for all the data
volume files in the VLF (see example).
A brain mask volume is the same size as a data volume and has voxel values of 0's (non-brain voxels)
and 1's (brain voxels). The brain mask is used by various analysis programs to determine which voxels
to keep for analysis.
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An integer specifying the population that a volume belongs to (e.g - normal, ataxia). Each different
population should have its own unique number. Typically, 0 is reserved for normals, but this is not a requirment.
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An integer specifying the protocol under which the volume was acquired (e.g, finger tapping). The same
protocol number is assigned to all volumes in a scan session, regardless of what the subject was doing
during the acquisition of the volume (e.g, baseline or some motor task). The specific task performed during
each scan is usually encoded in the Brain State field.
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An integer that uniquely identifies the subject who was scanned. All volumes from the same scan session will
have the same subject number.
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An integer that uniquely identifies the scan session. All volumes from the same scan session will have the
same session number.
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An integer specifying the ordinal value of the volume within the scan session. The first volume in the session
is assigned 1, the second volume in the session is assigned 2, etc.
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An integer indicating the run from which a volume came from. A run is usually an fMRI term. For PET scans a run
can be a set of scans within a session whose task sequence is repeated. For example, a session of 8 scans
consisting of task1, task2, task1, task2, task1, task2, task1, task2 can be divided into 4 runs: 1) scan1, scan2,
2) scan3, scan4, 3) scan5, scan6, and 4) scan7, scan8. We could also have 2 runs consisting of 4 scans each: 1)
scan1, scan2, scan3, scan4, and 2) scan4, scan5, scan6, scan7, scan8.
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An integer specifying the task being performed during the scan. For example, a BABABABA scan session (B=
baseline, A=activation) could have brain states values of 0,1,0,1,0,1,0,1. Zero is typically reserved for
baseline scans.
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The subject's age. Use 0 if the age is unknown.
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The subject's sex. Use M for male, F for female, and U for unknown.
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The subject's weight in kilograms. Use 0 if the weight is unkown.
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Amount of radioactivity administered. This is primarily used to dose/weight normalize volumes prior to
analysis. This field has no meaning for modalities that do not deliver radioactivity (e.g - fMRI).
Use 0 if the dose is unknown.
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This field can be used to hold any numeric value the user wishes. It might hold performance measurements
taken during the scan or encode the handedness of the subjects (0 for right, 1 for left).
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Additional miscellaneous field.
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Additional miscellaneous field.
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Keyword=Value
Currently, there are 2 keyword/value pairs that can be specified in a volume
list file:
VOLSUFF=data_volume_suffix
The VOLSUFF value is appended to all the data volume names, and MSKSUFF value
is appended to all the mask volume names in the list file. This is sometimes
convenient if all the volume names share a common filename suffix.
Volume Number
Data Volume Name
Mask Volume Name
Population
Protocol
Subject
Scan Session
Scan Number
Run
Brain State
Subject's Age
Subject's Sex
Subject's Weight
Dosage
Miscellaneous 1
Miscellaneous 2
Miscellaneous 3
MSKSUFF=mask_volume_suffix