Caret6:FileNaming

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File Naming

Standard file naming is important in Caret6. First, a properly named file conveys important information about the file. Second, some operation in Caret6 will use the name of a file to create names for new files. If a file is not properly named, new files produced by Caret6 may be strangely named or possibly even cause the command to fail.

File Name Components

A properly named Caret file name consists of several components. Not all components are applicable to all types of files.

Individual components MUST NEVER contain a "." (period). Use "_" (underscore) if a component contains multiple words. For example, use task_finger_tap'" instead of "task.finger.tap".

subject/study

subject or study is short name identifying the subject (participant) or a study that contains multiple participants.

structure

structure is an abbreviation for the structure that the data file's contents represents.

Abbreviation Structure
ALL Any and All
C Cerebellum
L Left Cerebral Cortex
R Right Cerebral Cortex
LR Left and Right Cerebral Cortices

For a full list of structures and their abbreviations, run caret6_command -list-structures.

description

description short description that helps identify the contents of the data file. For surface files, the description typically describes the type of surface.

space

space is an abbreviation of the data's stereotaxic space.

Abbreviation Space Description
mni Montreal Neurological Institute

mesh

For an individual subject, mesh is the number of nodes. For an standard mesh, this value is the number of nodes (rounded to the nearest thousand) followed by the abbreviation of the standard mesh or atlas.

Abbreviation Mesh Description
74k_pals Population Average Landmark- and Surface-based atlas of cerebral cortex
74k_f99 Monkey F99 Atlas
164k_fs_L FreeSurfer fsaverage left hemisphere
164k_fs_R FreeSurfer fsaverage right hemisphere
164k_fs_LR FreeSurfer fsaverage hybrid left/right hemisphere

extension

A file system's extension identifies the file type and is used in file selection dialogs.

Required/Optional File Name Components by File Type

File Type Subject or

Study

Structure Description Space Mesh Extension Examples
Annotation R R R X a .annotation case01.R.brodmann.71785.annotation

pals.ALL.brodmann.74k_pals.annotation

Border Projection R R R X a .borderproj case01.R.visuotopic.71785.annotation

pals.ALL.visuotopic.74k_pals.annotation

Foci Projection R R R X a .fociproj case01.R.motion.71785.annotation

pals.ALL.motion.74k_pals.annotation

Foci Search X X R X X .focisearch visual_and_motion.focisearch
Label R R R X R .label.gii case01.R.geography.71785.label.gii
Metric R R R X R .func.gii case01.R.retinotopy.71785.func.gii
Multi-Resolution Morphing X X R X X .morph
Palette X X R X X .palette fidl.palette
Region of Interest - Surface R R R X R .region.gii case01.R.visual_areas.71785.region.gii
Registration Map - Surface R R R X R .register_map registered_to_colin.R.landmark_vector.73730.register_map
Scene R R R X X .scene
Scene - Generic O X R X X .scene_generic
Shape R R R X R .shape.gii case01.R.sulcal_depth.71785.shape.gii
Specification R R O X a .spec case01.R.spec

pals.ALL.autism.74k_pals.spec

Study Collection O X R X X .study_collection
Study Metadata O X R X X .study
Surface R R R b R .surf.gii
Vector R X R X a .vector.gii
Vocabulary X X R X X .vocabulary
Volume R R R R X .nii (uncompressed)

.nii.gz (compressed)


Notes:

  • O - Optional.
  • R - Required.
  • X - Not Allowed.
  • a - Required if file is for a single structure or if all structures have the same number of nodes.
  • b - Required if anatomical surface.

Surface File Description Values

For Anatomical Surfaces

  • midthickness (layer 4)
  • midthickness_mws (layer 4, medial wall smoothed)
  • pial
  • white

For Other Surfaces

  • ellipsoid
  • flat
  • inflated
  • spherical
  • spherical_std
  • very_inflated
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