afni_whereami: wrapper class for AFNI whereami

In UNCDEPENdLab/fmri.pipeline: Analysis of fMRI Data on HPC clusters

wrapper class for AFNI whereami

Description

wrapper class for AFNI whereami

wrapper class for AFNI whereami

Methods

Public methods

• afni_whereami$new()

• afni_whereami$get_call()

• afni_whereami$get_omask_call()

• afni_whereami$get_whereami_df()

• afni_whereami$get_overlap_df()

• afni_whereami$get_omask_df()

• afni_whereami$get_outputs()

• afni_whereami$run()

• afni_whereami$clone()

---

Method new()

create new afni_whereami object

Usage

afni_whereami$new(
  afni_3dclusterize_obj = NULL,
  omask = NULL,
  coord_file = NULL,
  coord_file_columns = NULL,
  coord_vector = NULL,
  atlases = NULL,
  coord_orientation = NULL,
  coord_space = NULL,
  output_file = NULL,
  omask_output_file = NULL,
  afnidir = NULL
)

Arguments

afni_3dclusterize_obj

Use an existing 3dClusterize object to build the whereami lookup

omask

Use this integer-valued cluster mask to lookup percent overlap with different atlas parcels

coord_file

The text file containing coordinates for the clusters to lookup

coord_file_columns

The columns in coord_file containing the x, y, and z coordinates. Note that these should be zero-based indices, so the first column is 0, second column is 1, etc.

coord_vector

Rather than lookup multiple locations from a file, coord_vector requires three numeric values (x, y, and z coordinates) that are used to lookup a single region in the atlases.

atlases

a character vector of atlases in whereami to use for lookup

coord_orientation

LPI or RAI

coord_space

The template space for the coordinates. Default: 'MNI'

output_file

The file name/path for the output of whereami

omask_output_file

The file name/path for the output of whereami with the omask (percentage overlap)

afnidir

The location of afni

---

Method get_call()

return the whereami call for this object

Usage

afni_whereami$get_call()

---

Method get_omask_call()

return the whereami call for the omask lookup

Usage

afni_whereami$get_omask_call()

---

Method get_whereami_df()

return the data.frame of coordinates and labels from the whereami lookup

Usage

afni_whereami$get_whereami_df()

---

Method get_overlap_df()

return the data.frame of percent overlap between each atlas and clusters/ROIs in the input mask

Usage

afni_whereami$get_overlap_df()

---

Method get_omask_df()

return the data.frame of the percentage overlap for each parcel (not implemented)

Usage

afni_whereami$get_omask_df()

---

Method get_outputs()

return a list of the output files from this whereami object

Usage

afni_whereami$get_outputs(exclude_missing = TRUE)

Arguments

exclude_missing

if TRUE, any expected output file that does not exist will be NA in the returned list

Returns

a list of all output files

---

Method run()

Run whereami for this object

Usage

afni_whereami$run(force = FALSE)

Arguments

force

if TRUE, re-run a whereami call even if the expected output file exists

---

Method clone()

The objects of this class are cloneable with this method.

Usage

afni_whereami$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

UNCDEPENdLab/fmri.pipeline documentation built on April 3, 2025, 3:21 p.m.