Region of interest specification files#

Region of interest (ROI) specification "names" files (*.names) are simple text files that provide information on what regions of interest to use in the analyses. They are used to define seeds when computing seed-based correlation maps, and to define regions from which to extract timecourses for ROI based analyses.

The first line in the names file provides a path to the group level mask file to be used for ROI definition. A mask file is a single volume image file in which each voxel is coded either with 0 or an integer code denoting a specific ROI. If no group level mask file is to be used, the first line should read none. Please note that you can use either absolute paths (paths starting with /) or relative paths (paths that do not start with /). In the latter case, the relative path should describe the location of the group mask file relative to the folder in which the .names file is. Relative paths are preferred when you expect that the relevant data might be moved (e.g. when sharing data across computers), whereas absolute paths are preferred when you would like to use different regions based on the same group mask image that is in a stable location.

Each of the following lines in the names file codes a single region and should provide the following information:

  1. The name of the ROI to be used in the analyses,

  2. the integer code (or codes) that corresponds to that ROI in the group level mask, and

  3. the integer code (or codes) to be used in subject-specific ROI mask files (usually listed in list files—see below).

The three types of information should be separated by a "pipe" symbol: |, whereas integer codes should be separated by a comma. If no code is specified for the group mask, a space should separate the two "pipe" symbols.


Here is an example of a names file:

LTh| |9
RTh| |48

The first line informs that the group level mask to be used is in /data/study1/ROI/master_mask.nii.gz. The second line specifies an ACC region, which is defined by an intersection of all the voxels marked with value 101 in the group level mask and all the voxels marked with values 3 or 42 (which correspond to left and right cortex in FreeSurfer aseg file, respectively) in the individual subject mask file. The third line specifies a DLPFC region. This one is defined by all the voxels that have value 108 in the group level mask file and is not further constrained by a subject-specific mask file. The fourth and fifth lines specify left thalamus and right thalamus regions. These are not constrained by a group level mask but rather defined only by codes 9 and 48 (referring to FreeSurfer codes for left and right thalamus, respectively) in a subject-specific mask file.

The specific coding in the names file allows a combination of group level and subject level masks. The final region is defined by a union of voxel codes within a mask file and an intersection of the resulting group level and subject-specific masks. If no value is provided for a mask file, all voxels from that mask are used. This system allows you to define a priori the ROI to be used in the analysis, but then further makes sure that in each individual only the voxels that are within a specific subject specific area (e.g. only gray matter voxels) are included in the analyses.

When the subject specific file is a FreeSurfer generated aseg or aseg+aparc file, to ease specification of relevant regions, the following names can be used instead of listing all the relevant codes:

  • lcgray (left cortex gray matter)

  • rcgray (right cortex gray matter)

  • cgray (cortical gray matter)

  • lsubc (left subcortical gray matter)

  • rsubc (right subcortical gray matter)

  • subc (subcortical gray matter)

  • lcerc (left cerebellar gray matter)

  • rcerc (right cerebellar gray matter)

  • cerc (cerebral gray matter)

  • lgray (left hemisphere gray matter)

  • rgray (right hemisphere gray matter)

  • gray (whole brain gray matter)

The above example could then be rewritten as:

LTh| |9
RTh| |48

Note: The names are only valid when the subject level mask is a FreeSurfer generated aseg or aseg+aparc file.

Names files get their names from the .names extension.