Title: | Wrapper Functions for 'Freesurfer' |
---|---|
Description: | Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output. |
Authors: | John Muschelli [aut, cre] , Athanasia Mo Mowinckel [ctb] |
Maintainer: | John Muschelli <[email protected]> |
License: | GPL-3 |
Version: | 1.6.10 |
Built: | 2024-11-11 03:13:53 UTC |
Source: | https://github.com/muschellij2/freesurfer |
Converts Freesurfer aparcs table to brainGraph naming
convention, relying on aparcstats2table
aparcs_to_bg(subjects, measure, ...)
aparcs_to_bg(subjects, measure, ...)
subjects |
subjects to analyze,
passed to |
measure |
measure to be analyzed,
passed to |
... |
additional arguments passed to |
Long data.frame
if (have_fs()) { fs_subj_dir() df = aparcs_to_bg(subjects = "bert", measure = "thickness") print(head(df)) }
if (have_fs()) { fs_subj_dir() df = aparcs_to_bg(subjects = "bert", measure = "thickness") print(head(df)) }
This function calls aparcstats2table
to
convert parcellation statistics to a table
aparcstats2table( subjects, outfile = NULL, hemi = c("lh", "rh"), measure = c("area", "volume", "thickness", "thicknessstd", "meancurv", "gauscurv", "foldind", "curvind"), sep = c("tab", "space", "comma", "semicolon"), parc = c("aparc", "aparc.a2009s"), skip = FALSE, subj_dir = NULL, opts = "", verbose = TRUE )
aparcstats2table( subjects, outfile = NULL, hemi = c("lh", "rh"), measure = c("area", "volume", "thickness", "thicknessstd", "meancurv", "gauscurv", "foldind", "curvind"), sep = c("tab", "space", "comma", "semicolon"), parc = c("aparc", "aparc.a2009s"), skip = FALSE, subj_dir = NULL, opts = "", verbose = TRUE )
subjects |
(character) vector of subjects |
outfile |
(character) output filename |
hemi |
(character) hemisphere to run statistics |
measure |
(character) measure to be calculated |
sep |
(character) separator for the output file. This will be
an attribute of |
parc |
(character) parcellation to compute on |
skip |
(logical) if subject does not have parcellation,
should the command skip that subject ( |
subj_dir |
(character path) if a different subjects directory
is to be used other than |
opts |
(character) additional options to |
verbose |
(logical) print diagnostic messages |
Character filename of output file, with the attribute of the separator
if (have_fs()) { fs_subj_dir() outfile = aparcstats2table(subjects = "bert", hemi = "lh", meas = "thickness") }
if (have_fs()) { fs_subj_dir() outfile = aparcstats2table(subjects = "bert", hemi = "lh", meas = "thickness") }
This calls Freesurfer's aparcstats2table
help
aparcstats2table.help()
aparcstats2table.help()
Result of fs_help
This function calls asegstats2table
to
convert parcellation statistics to a table
asegstats2table( subjects = NULL, inputs = NULL, outfile = NULL, measure = c("volume", "mean", "std"), sep = c("tab", "space", "comma", "semicolon"), skip = FALSE, subj_dir = NULL, opts = "", verbose = TRUE )
asegstats2table( subjects = NULL, inputs = NULL, outfile = NULL, measure = c("volume", "mean", "std"), sep = c("tab", "space", "comma", "semicolon"), skip = FALSE, subj_dir = NULL, opts = "", verbose = TRUE )
subjects |
(character) vector of subjects |
inputs |
(character paths) vector of input filenames,
e.g. |
outfile |
(character) output filename |
measure |
(character) measure to be calculated |
sep |
(character) separator for the output file. This will be
an attribute of |
skip |
(logical) if subject does not have parcellation,
should the command skip that subject ( |
subj_dir |
(character path) if a different subjects directory
is to be used other than |
opts |
(character) additional options to |
verbose |
(logical) print diagnostic messages |
Character filename of output file, with the attribute of the separator
if (have_fs()) { outfile = asegstats2table(subjects = "bert", meas = "mean") }
if (have_fs()) { outfile = asegstats2table(subjects = "bert", meas = "mean") }
This calls Freesurfer's asegstats2table
help
asegstats2table.help()
asegstats2table.help()
Result of fs_help
Checks the Freesurfer system command result and will stop or warning based on whether output files exist.
check_fs_result(res, fe_before, fe_after)
check_fs_result(res, fe_before, fe_after)
res |
(numeric) Result from system command |
fe_before |
(logical) did the output file exist before the command ran |
fe_after |
(logical) did the output file exist after the command ran |
No return value, called for side effects
Ensures the output to be a character filename (or vector)
from an input image or nifti
to have .mnc
extension and
be converted to MNC when necessary
checkmnc(file, ...) ## S4 method for signature 'nifti' checkmnc(file, ...) ## S4 method for signature 'character' checkmnc(file, ...) ## S4 method for signature 'list' checkmnc(file, ...) ensure_mnc(file, ...)
checkmnc(file, ...) ## S4 method for signature 'nifti' checkmnc(file, ...) ## S4 method for signature 'character' checkmnc(file, ...) ## S4 method for signature 'list' checkmnc(file, ...) ensure_mnc(file, ...)
file |
character or |
... |
options passed to |
Character filename of mnc image
John Muschelli [email protected]
This function copies files specified by the types of data, determined by the folder Freesurfer put them in, into a temporary directory for easier separation of data and different structuring of data.
construct_subj_dir( label = NULL, mri = NULL, stats = NULL, surf = NULL, touch = NULL, subj = NULL, subj_root_dir = tempdir() )
construct_subj_dir( label = NULL, mri = NULL, stats = NULL, surf = NULL, touch = NULL, subj = NULL, subj_root_dir = tempdir() )
label |
Files to copy to |
mri |
Files to copy to |
stats |
Files to copy to |
surf |
Files to copy to |
touch |
Files to copy to |
subj |
Name of subject to make folder for to use for Freesurfer functions.
If |
subj_root_dir |
Directory to put folder with contents of |
List with the subject name, the SUBJECTS_DIR to use (the directory that contains the subject name), and the types of objects copied
## Not run: library(freesurfer) label = "/Applications/freesurfer/subjects/bert/label/aparc.annot.a2009s.ctab" mri = c( "/Applications/freesurfer/subjects/bert/mri/aparc.a2009s+aseg.mgz", "/Applications/freesurfer/subjects/bert/mri/aseg.auto.mgz") stats = c("/Applications/freesurfer/subjects/bert/stats/lh.aparc.stats", "/Applications/freesurfer/subjects/bert/stats/aseg.stats") surf = "/Applications/freesurfer/subjects/bert/surf/lh.thickness" touch = NULL ## End(Not run)
## Not run: library(freesurfer) label = "/Applications/freesurfer/subjects/bert/label/aparc.annot.a2009s.ctab" mri = c( "/Applications/freesurfer/subjects/bert/mri/aparc.a2009s+aseg.mgz", "/Applications/freesurfer/subjects/bert/mri/aseg.auto.mgz") stats = c("/Applications/freesurfer/subjects/bert/stats/lh.aparc.stats", "/Applications/freesurfer/subjects/bert/stats/aseg.stats") surf = "/Applications/freesurfer/subjects/bert/surf/lh.thickness" touch = NULL ## End(Not run)
Reads in a surface file from Freesurfer and separates into vertices and faces
convert_surface(infile, ...)
convert_surface(infile, ...)
infile |
Input surface file |
... |
additional arguments to pass to
|
List of 3 elements: a header indicating the number of vertices and faces, the vertices, and the faces
This was adapted from the gist: https://gist.github.com/mm–/4a4fc7badacfad874102
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") res = convert_surface(infile = infile) }
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") res = convert_surface(infile = infile) }
Reads a Freesurfer curvature file according to the FREESURFER_HOME/matlab/read_curv.m file.
freesurfer_read_curv(file)
freesurfer_read_curv(file)
file |
file name of a curvature file |
Numeric vector
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") fid = file(file, open = "rb") out = freesurfer_read_curv(file) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") fid = file(file, open = "rb") out = freesurfer_read_curv(file) }
Reads a Freesurfer Surface file from
the surf/
directory
from recon-all
freesurfer_read_surf(file)
freesurfer_read_surf(file)
file |
surface file (e.g. |
List of length 2: vertices and faces are the elements
if (have_fs()) { fname = file.path(fs_subj_dir(), "bert", "surf", "lh.inflated") out = freesurfer_read_surf(fname) }
if (have_fs()) { fname = file.path(fs_subj_dir(), "bert", "surf", "lh.inflated") out = freesurfer_read_surf(fname) }
Reads first 3 records of file and returns the rotated value, for checking for other functions.
freesurfer_read3(file)
freesurfer_read3(file)
file |
thickness file or anything in surf/ directory from Freesurfer subject |
Numeric
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") out = freesurfer_read3(file) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") out = freesurfer_read3(file) }
Reads first 3 records from a connection and returns the rotated value, for checking for other functions.
freesurfer_read3_con(fid)
freesurfer_read3_con(fid)
fid |
connection to a thickness file or anything in surf/ directory from Freesurfer subject |
Numeric
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") fid = file(file, open = "rb") out = freesurfer_read3_con(file) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert", "surf") file = file.path(bert_dir, "lh.thickness") fid = file(file, open = "rb") out = freesurfer_read3_con(file) }
Finds the FREESURFER_HOME from system environment or
getOption("freesurfer.path")
for location of Freesurfer functions and returns it
freesurferdir() freesurfer_dir() fs_dir()
freesurferdir() freesurfer_dir() fs_dir()
Character path
if (have_fs()) { freesurferdir() freesurfer_dir() fs_dir() }
if (have_fs()) { freesurferdir() freesurfer_dir() fs_dir() }
This function calls Freesurfer command passed to func
fs_cmd( func, file, outfile = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, samefile = FALSE, opts_after_outfile = FALSE, frontopts = "", add_ext = TRUE, bin_app = "bin", ... )
fs_cmd( func, file, outfile = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, samefile = FALSE, opts_after_outfile = FALSE, frontopts = "", add_ext = TRUE, bin_app = "bin", ... )
func |
(character) Freesurfer function |
file |
(character) image to be manipulated |
outfile |
(character) resultant image name (optional) |
retimg |
(logical) return image of class nifti |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) to be passed to |
opts |
(character) operations to be passed to |
verbose |
(logical) print out command before running |
samefile |
(logical) is the output the same file? |
opts_after_outfile |
(logical) should |
frontopts |
(character) options/character to put in before filename |
add_ext |
(logical) should the extension be added to
the |
bin_app |
(character) appendix to add to |
... |
additional arguments passed to |
If retimg
then object of class nifti. Otherwise,
Result from system command, depends if intern is TRUE or FALSE.
This function takes in the function and returns the help from Freesurfer for that function
fs_help(func_name, help.arg = "--help", extra.args = "", ...)
fs_help(func_name, help.arg = "--help", extra.args = "", ...)
func_name |
Freesurfer function name |
help.arg |
Argument to print help, usually "–help" |
extra.args |
Extra arguments to be passed other than
|
... |
additional arguments to |
Prints help output and returns output as character vector
if (have_fs()) { fs_help(func_name = "mri_watershed") }
if (have_fs()) { fs_help(func_name = "mri_watershed") }
Runs get_fs_output()
to extract FSLOUTPUTTYPE and then
gets corresponding extension (such as .nii.gz)
fs_imgext()
fs_imgext()
Extension for output type
fs_imgext()
fs_imgext()
A data.frame
with the index, label,
and RGBA (red, blue, green, alpha) specification for the segmentations
fs_lut
fs_lut
An object of class data.frame
with 1266 rows and 6 columns.
Finds the SUBJECTS_DIR from system environment or
getOption("fs.subj_dir")
for subjects dir
fs_subj_dir()
fs_subj_dir()
SUBJECTS_DIR, such as ${FREESURFER_HOME}/subjects
if (have_fs()) { fs_subj_dir() }
if (have_fs()) { fs_subj_dir() }
Finds the Freesurfer version from FREESURFER_HOME/build-stamp.txt
fs_version()
fs_version()
If the version file does not exist, it will throw a warning, but it will return an empty string. Otherwise it will be a string of the version.
This will use fs_dir()
to get the directory of FREESURFER
if (have_fs()) { fs_version() }
if (have_fs()) { fs_version() }
Finds the Freesurfer from system environment or getOption("freesurfer.path")
for location of Freesurfer functions
get_fs(bin_app = c("bin", "mni/bin", ""))
get_fs(bin_app = c("bin", "mni/bin", ""))
bin_app |
Should |
NULL if Freesurfer in path, or bash code for setting up Freesurfer DIR
This will use Sys.getenv("FREESURFER_HOME")
before getOption("freesurfer.path")
.
If the directory is not found for Freesurfer in Sys.getenv("FreesurferDIR")
and
getOption("freesurfer.path")
, it will try the default directory /usr/local/freesurfer
.
if (have_fs()) { get_fs() }
if (have_fs()) { get_fs() }
Finds the FSF_OUTPUT_FORMAT from system environment or
getOption("fs.outputtype")
for output type (nii.gz, nii, ANALYZE,etc)
get_fs_output()
get_fs_output()
FSF_OUTPUT_FORMAT, such as nii.gz If none found, uses nii.gz as default
get_fs_output()
get_fs_output()
Uses get_fs
to check if FreesurferDIR is accessible or the option
freesurfer.path
is set and returns logical
have_fs(..., check_license = FALSE)
have_fs(..., check_license = FALSE)
... |
options to pass to |
check_license |
Should a license file be checked to exist? |
Logical TRUE is Freesurfer is accessible, FALSE if not
have_fs()
have_fs()
This function calls mnc2nii
to convert MNC files to NIfTI
mnc2nii(file, outfile = NULL)
mnc2nii(file, outfile = NULL)
file |
(character) input filename |
outfile |
(character) output filename |
Character filename of output
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mnc = nii2mnc(img) img_file = mnc2nii(mnc, outfile = tempfile(fileext = ".nii")) neurobase::readnii(img_file, verbose = TRUE) }
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mnc = nii2mnc(img) img_file = mnc2nii(mnc, outfile = tempfile(fileext = ".nii")) neurobase::readnii(img_file, verbose = TRUE) }
This calls Freesurfer's mnc2nii
help
mnc2nii.help()
mnc2nii.help()
Result of fs_help
This function calls mri_convert
to convert an image
mri_convert(file, outfile, opts = "")
mri_convert(file, outfile, opts = "")
file |
(character) input filename |
outfile |
(character) output filename |
opts |
(character) additional options to |
Result of system
command
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) res = mri_convert(img, outfile = tempfile(fileext = ".mgz")) }
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) res = mri_convert(img, outfile = tempfile(fileext = ".mgz")) }
This calls Freesurfer's mri_convert
help
mri_convert.help()
mri_convert.help()
Result of fs_help
This calls Freesurfer's mri_deface
mri_deface(file, brain_template = NULL, face_template = NULL, ...)
mri_deface(file, brain_template = NULL, face_template = NULL, ...)
file |
File to pass to |
brain_template |
|
face_template |
|
... |
Additional arguments to pass to |
Result of fs_cmd
, which type depends on
arguments to ...
If brain_template
orface_template
is NULL
,
they will be downloaded.
if (have_fs()){ base_url = "https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface" url = file.path(base_url, "sample_T1_input.mgz") x = tempfile(fileext = ".mgz") out = try({ utils::download.file(url, destfile = x) }) if (!inherits(out, "try-error")) { noface = mri_deface(x) } else { url = paste0( "https://raw.githubusercontent.com/muschellij2/kirby21.t1/master/", "inst/visit_1/113/113-01-T1.nii.gz") x = tempfile(fileext = ".nii.gz") out = try({ utils::download.file(url, destfile = x) }) noface = mri_deface(x) } }
if (have_fs()){ base_url = "https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface" url = file.path(base_url, "sample_T1_input.mgz") x = tempfile(fileext = ".mgz") out = try({ utils::download.file(url, destfile = x) }) if (!inherits(out, "try-error")) { noface = mri_deface(x) } else { url = paste0( "https://raw.githubusercontent.com/muschellij2/kirby21.t1/master/", "inst/visit_1/113/113-01-T1.nii.gz") x = tempfile(fileext = ".nii.gz") out = try({ utils::download.file(url, destfile = x) }) noface = mri_deface(x) } }
This calls Freesurfer's mri_info
mri_info(file, ...)
mri_info(file, ...)
file |
File to pass to |
... |
Additional arguments to pass to |
Result of fs_cmd
, which type depends on
arguments to ...
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)){ img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mri_info(img) }
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)){ img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mri_info(img) }
This calls Freesurfer's mri_info
help
mri_info.help()
mri_info.help()
Result of fs_help
This function calls mri_mask
to mask an image
mri_mask(file, mask, outfile = NULL, retimg = TRUE, opts = "", ...)
mri_mask(file, mask, outfile = NULL, retimg = TRUE, opts = "", ...)
file |
(character) input filename |
mask |
(character) mask filename |
outfile |
(character) output filename |
retimg |
(logical) return image of class nifti |
opts |
(character) additional options to |
... |
additional arguments passed to |
Character or nifti depending on retimg
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mask = img > 1 res = mri_mask(img, mask) }
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mask = img > 1 res = mri_mask(img, mask) }
This calls Freesurfer's mri_mask
help
mri_mask.help()
mri_mask.help()
Result of fs_help
This function calls mri_normalize
to normalize the
values of the image, with white matter voxels around 110.
mri_normalize(file, outfile = NULL, retimg = TRUE, opts = "", ...)
mri_normalize(file, outfile = NULL, retimg = TRUE, opts = "", ...)
file |
(character) input filename |
outfile |
(character) output filename |
retimg |
(logical) return image of class nifti |
opts |
(character) additional options to |
... |
additional arguments passed to |
Character or nifti depending on retimg
## Not run: if (have_fs()){ mri_normalize("/path/to/T1.nii.gz") } ## End(Not run)
## Not run: if (have_fs()){ mri_normalize("/path/to/T1.nii.gz") } ## End(Not run)
This calls Freesurfer's mri_normalize
help
mri_normalize.help()
mri_normalize.help()
Result of fs_help
This function calls mri_segment
to segment tissues from an image
mri_segment(file, outfile = NULL, retimg = TRUE, opts = "", ...)
mri_segment(file, outfile = NULL, retimg = TRUE, opts = "", ...)
file |
(character) input filename |
outfile |
(character) output filename |
retimg |
(logical) return image of class nifti |
opts |
(character) additional options to |
... |
additional arguments passed to |
Character or nifti depending on retimg
NOT COMPLETE
This calls Freesurfer's mri_segment
help
mri_segment.help()
mri_segment.help()
Result of fs_help
mri_surf2surf
function to
resamples one cortical surface onto anotherThis function calls Freesurfer mri_surf2surf
to
resample one cortical surface onto another
mri_surf2surf( subject = NULL, target_subject = NULL, trg_type = c("curv", "w", "mgh", "nii"), src_type = c("curv", "w"), outfile = NULL, hemi = c("lh", "rh"), sval = c("thickness"), subj_dir = NULL, opts = "", verbose = TRUE )
mri_surf2surf( subject = NULL, target_subject = NULL, trg_type = c("curv", "w", "mgh", "nii"), src_type = c("curv", "w"), outfile = NULL, hemi = c("lh", "rh"), sval = c("thickness"), subj_dir = NULL, opts = "", verbose = TRUE )
subject |
(character) vector of subject name |
target_subject |
(character) vector of target subject name |
trg_type |
(character) target file type, can be curv, paint (w), mgh, or nii |
src_type |
(character) source file type, can be curv or paint (w) |
outfile |
(character) output filename |
hemi |
(character) hemisphere to run statistics |
sval |
(character) source file |
subj_dir |
(character path) if a different subjects directory
is to be used other than |
opts |
(character) additional options to |
verbose |
(logical) print diagnostic messages |
Name of output file
if (have_fs()) { out = mri_surf2surf( subject = 'bert', target_subject = 'fsaverage', trg_type = 'curv', src_type = 'curv', hemi = "rh", sval = "thickness") }
if (have_fs()) { out = mri_surf2surf( subject = 'bert', target_subject = 'fsaverage', trg_type = 'curv', src_type = 'curv', hemi = "rh", sval = "thickness") }
This calls Freesurfer's mri_surf2surf
help
mri_surf2surf.help()
mri_surf2surf.help()
Result of fs_help
This function calls mri_watershed
to extract a brain
from an image, usually for skull stripping.
mri_watershed(file, outfile = NULL, retimg = TRUE, opts = "", ...)
mri_watershed(file, outfile = NULL, retimg = TRUE, opts = "", ...)
file |
(character) input filename |
outfile |
(character) output filename |
retimg |
(logical) return image of class nifti |
opts |
(character) additional options to |
... |
additional arguments passed to |
Character or nifti depending on retimg
## Not run: if (have_fs()){ mri_watershed("/path/to/T1.nii.gz") } ## End(Not run)
## Not run: if (have_fs()){ mri_watershed("/path/to/T1.nii.gz") } ## End(Not run)
This calls Freesurfer's mri_watershed
help
mri_watershed.help()
mri_watershed.help()
Result of fs_help
This function call mris_convert
, a
general conversion program for converting between cortical surface file formats
mris_convert(infile, outfile = NULL, ext = ".asc", opts = "", verbose = TRUE)
mris_convert(infile, outfile = NULL, ext = ".asc", opts = "", verbose = TRUE)
infile |
(character) file path for input file |
outfile |
(character) output file path |
ext |
(character) output file extension, default is set to .asc |
opts |
(character) additional options to add to front of command |
verbose |
(logical) print diagnostic messages |
Name of output file
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert( infile = file.path(bert_surf_dir, "lh.white") ) }
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert( infile = file.path(bert_surf_dir, "lh.white") ) }
This function call mris_convert
,
using the --annot
option
mris_convert_annot(annot, opts = "", ...)
mris_convert_annot(annot, opts = "", ...)
annot |
(character) annotation or gifti label data |
opts |
(character) additional options to
|
... |
additional arguments to |
Result of mris_convert
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") gii_file = mris_convert_annot( infile = file.path(bert_dir, "surf", "lh.white"), annot = file.path(bert_dir, "label", "lh.aparc.annot"), ext = ".gii" ) gii = mris_convert_annot( infile = file.path(bert_dir, "surf", "lh.white"), annot = gii_file, ext = ".gii" ) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") gii_file = mris_convert_annot( infile = file.path(bert_dir, "surf", "lh.white"), annot = file.path(bert_dir, "label", "lh.aparc.annot"), ext = ".gii" ) gii = mris_convert_annot( infile = file.path(bert_dir, "surf", "lh.white"), annot = gii_file, ext = ".gii" ) }
This function call mris_convert
,
using the -c
option
mris_convert_curv(curv, opts = "", ...)
mris_convert_curv(curv, opts = "", ...)
curv |
(character) scalar curv overlay file |
opts |
(character) additional options to
|
... |
additional arguments to |
Result of mris_convert
The filename of the output may change due to how Freesurfer does curvature conversions and you may need to paste the prefix to get the correct filename, as seen in the example.
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert_curv( infile = file.path(bert_surf_dir, "lh.white"), curv = file.path(bert_surf_dir, "lh.thickness") ) if (!file.exists(asc_file)) { asc_file = file.path(dirname(asc_file), paste0("lh.", basename(asc_file))) } res = read_fs_table(asc_file, header = FALSE) colnames(res) = c("index", "coord_1", "coord_2", "coord_3", "value") head(res) }
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert_curv( infile = file.path(bert_surf_dir, "lh.white"), curv = file.path(bert_surf_dir, "lh.thickness") ) if (!file.exists(asc_file)) { asc_file = file.path(dirname(asc_file), paste0("lh.", basename(asc_file))) } res = read_fs_table(asc_file, header = FALSE) colnames(res) = c("index", "coord_1", "coord_2", "coord_3", "value") head(res) }
This function call mris_convert
,
using the -n
option
mris_convert_normals(opts = "", ...)
mris_convert_normals(opts = "", ...)
opts |
(character) additional options to
|
... |
additional arguments to |
Result of mris_convert
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") asc_file = mris_convert_normals( infile = file.path(bert_dir, "surf", "lh.white") ) readLines(asc_file, n = 6) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") asc_file = mris_convert_normals( infile = file.path(bert_dir, "surf", "lh.white") ) readLines(asc_file, n = 6) }
This function call mris_convert
,
using the -v
option
mris_convert_vertex(opts = "", ...)
mris_convert_vertex(opts = "", ...)
opts |
(character) additional options to
|
... |
additional arguments to |
Result of mris_convert
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert_vertex( infile = file.path(bert_surf_dir, "lh.white") ) readLines(asc_file, n = 6) }
if (have_fs()) { bert_surf_dir = file.path(fs_subj_dir(), "bert", "surf") asc_file = mris_convert_vertex( infile = file.path(bert_surf_dir, "lh.white") ) readLines(asc_file, n = 6) }
This calls Freesurfer's mris_convert
help
mris_convert.help()
mris_convert.help()
Result of fs_help
This function calls mris_euler_number
to
calculate the Euler Number
mris_euler_number(file, outfile = NULL, opts = "")
mris_euler_number(file, outfile = NULL, opts = "")
file |
(character) input filename |
outfile |
(character) output filename |
opts |
(character) additional options to |
Result of system
command
## Not run: if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) res = mris_euler_number(img, outfile = tempfile(fileext = ".mgz")) } ## End(Not run)
## Not run: if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) res = mris_euler_number(img, outfile = tempfile(fileext = ".mgz")) } ## End(Not run)
This calls Freesurfer's mris_euler_number
help
mris_euler_number.help()
mris_euler_number.help()
Result of fs_help
This function calls nii2mnc
to convert NIfTI to MNC files
nii2mnc(file, outfile = NULL)
nii2mnc(file, outfile = NULL)
file |
(character) input filename |
outfile |
(character) output filename |
Character filename of output
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mnc = nii2mnc(img) img_file = mnc2nii(mnc) }
if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) { img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5))) mnc = nii2mnc(img) img_file = mnc2nii(mnc) }
This calls Freesurfer's mnc2nii
help
nii2mnc.help()
nii2mnc.help()
Result of fs_help
This function calls nu_correct
to correct for non-uniformity
nu_correct(file, mask = NULL, opts = "", verbose = TRUE, ...)
nu_correct(file, mask = NULL, opts = "", verbose = TRUE, ...)
file |
(character) input filename |
mask |
(character or nifti) Mask to use for correction. |
opts |
(character) additional options to |
verbose |
print diagnostic messages |
... |
additional arguments passed to |
Object of class nifti depending on retimg
## Not run: if (have_fs()){ nu_correct("/path/to/T1.nii.gz") } ## End(Not run)
## Not run: if (have_fs()){ nu_correct("/path/to/T1.nii.gz") } ## End(Not run)
This calls Freesurfer's nu_correct
help
nu_correct.help()
nu_correct.help()
Result of fs_help
Reads Freesurfer binary annotation files that contain information on vertex labels and colours for use in analyses and brain area lookups.
read_annotation(path, verbose = TRUE)
read_annotation(path, verbose = TRUE)
path |
path to annotation file, usually with extension |
verbose |
logical. |
This function is heavily based on Freesurfer's read_annotation.m Original Author: Bruce Fischl CVS Revision Info: $Author: greve $ $Date: 2014/02/25 19:54:10 $ $Revision: 1.10 $
list of 3 with vertices, labels, and colortable
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") annot_file = file.path(bert_dir, "label", "lh.aparc.annot") res = read_annotation(annot_file) }
if (have_fs()) { bert_dir = file.path(fs_subj_dir(), "bert") annot_file = file.path(bert_dir, "label", "lh.aparc.annot") res = read_annotation(annot_file) }
Reads an aseg.stats
file from an individual subject
read_aseg_stats(file)
read_aseg_stats(file)
file |
aseg.stats file from Freesurfer |
List of 2 data.frame
s, one with the global measures and one
with the structure-specific measures.
if (have_fs()) { file = file.path(fs_subj_dir(), "bert", "stats", "aseg.stats") out = read_aseg_stats(file) }
if (have_fs()) { file = file.path(fs_subj_dir(), "bert", "stats", "aseg.stats") out = read_aseg_stats(file) }
Reads an label
file from an individual subject
read_fs_label(file)
read_fs_label(file)
file |
label file from Freesurfer |
data.frame
with 5 columns:
vertex_num
:Vertex Number
r_coord
:Coordinate in RL direction
a_coord
:Coordinate in AP direction
s_coord
:Coordinate in SI direction
value
:Value of label (depends on file)
if (have_fs()) { file = file.path(fs_subj_dir(), "bert", "label", "lh.BA1.label") if (!file.exists(file)) { file = file.path(fs_subj_dir(), "bert", "label", "lh.BA1_exvivo.label") } out = read_fs_label(file) }
if (have_fs()) { file = file.path(fs_subj_dir(), "bert", "label", "lh.BA1.label") if (!file.exists(file)) { file = file.path(fs_subj_dir(), "bert", "label", "lh.BA1_exvivo.label") } out = read_fs_label(file) }
This function reads output from a Freesurfer table command,
e.g. aparcstats2table
, asegstats2table
read_fs_table(file, sep = NULL, stringsAsFactors = FALSE, header = TRUE, ...)
read_fs_table(file, sep = NULL, stringsAsFactors = FALSE, header = TRUE, ...)
file |
(character path) filename of text file |
sep |
separator to override attribute of file, to
pass to |
stringsAsFactors |
(logical) passed to |
header |
Is there a header in the data |
... |
additional arguments to |
data.frame
from the file
if (have_fs()) { outfile = aparcstats2table(subjects = "bert", hemi = "lh", meas = "thickness") df = read_fs_table(outfile) seg_outfile = asegstats2table(subjects = "bert", meas = "mean") df_seg = read_fs_table(seg_outfile) } ## Not run: ### using the pipe if (requireNamespace("magrittr", quietly = TRUE)) { df_seg = asegstats2table(subjects = "bert", meas = "mean") %>% read_fs_table } ## End(Not run)
if (have_fs()) { outfile = aparcstats2table(subjects = "bert", hemi = "lh", meas = "thickness") df = read_fs_table(outfile) seg_outfile = asegstats2table(subjects = "bert", meas = "mean") df_seg = read_fs_table(seg_outfile) } ## Not run: ### using the pipe if (requireNamespace("magrittr", quietly = TRUE)) { df_seg = asegstats2table(subjects = "bert", meas = "mean") %>% read_fs_table } ## End(Not run)
This function calls mri_convert
to convert MGH/MGZ files to NIfTI, then reads it in using
readnii
readmgz(file) readmgh(file)
readmgz(file) readmgh(file)
file |
(character) input filename |
Object of class nifti
This function calls mnc2nii
to convert MNC files to NIfTI, then reads it in using
readnii
readmnc(file)
readmnc(file)
file |
(character) input filename |
Object of class nifti
Reconstruction from Freesurfer with most of the options implemented.
recon( infile, outdir = NULL, subjid, motioncor = TRUE, nuintensitycor = TRUE, talairach = TRUE, normalization = TRUE, skullstrip = TRUE, gcareg = TRUE, canorm = TRUE, careg = TRUE, rmneck = TRUE, skull_lta = TRUE, calabel = TRUE, normalization2 = TRUE, segmentation = TRUE, fill = TRUE, tessellate = TRUE, smooth1 = TRUE, inflate1 = TRUE, qsphere = TRUE, fix = TRUE, finalsurfs = TRUE, smooth2 = TRUE, inflate2 = TRUE, cortribbon = TRUE, sphere = TRUE, surfreg = TRUE, contrasurfreg = TRUE, avgcurv = TRUE, cortparc = TRUE, parcstats = TRUE, cortparc2 = TRUE, parcstats2 = TRUE, aparc2aseg = TRUE, verbose = TRUE, opts = "" )
recon( infile, outdir = NULL, subjid, motioncor = TRUE, nuintensitycor = TRUE, talairach = TRUE, normalization = TRUE, skullstrip = TRUE, gcareg = TRUE, canorm = TRUE, careg = TRUE, rmneck = TRUE, skull_lta = TRUE, calabel = TRUE, normalization2 = TRUE, segmentation = TRUE, fill = TRUE, tessellate = TRUE, smooth1 = TRUE, inflate1 = TRUE, qsphere = TRUE, fix = TRUE, finalsurfs = TRUE, smooth2 = TRUE, inflate2 = TRUE, cortribbon = TRUE, sphere = TRUE, surfreg = TRUE, contrasurfreg = TRUE, avgcurv = TRUE, cortparc = TRUE, parcstats = TRUE, cortparc2 = TRUE, parcstats2 = TRUE, aparc2aseg = TRUE, verbose = TRUE, opts = "" )
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
motioncor |
When there are multiple source volumes, this step will correct for small motions between them and then average them together. The input are the volumes found in file(s) mri/orig/XXX.mgz. The output will be the volume mri/orig.mgz. If no runs are found, then it looks for a volume in mri/orig (or mri/orig.mgz). If that volume is there, then it is used in subsequent processes as if it was the motion corrected volume. If no volume is found, then the process exits with errors. |
nuintensitycor |
Non-parametric Non-uniform intensity Normalization (N3), corrects for intensity non-uniformity in MR data, making relatively few assumptions about the data. This runs the MINC tool 'nu_correct'. By default, four iterations of nu_correct are run. The flag '-nuiterations' specification of some other number of iterations. |
talairach |
computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal. Creates the files mri/transform/talairach.auto.xfm and talairach.xfm. |
normalization |
Performs intensity normalization of the orig volume and places the result in mri/T1.mgz |
skullstrip |
Removes the skull from mri/T1.mgz and stores the result in mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed program. |
gcareg |
Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average. Creates the file mri/transforms/talairach.lta. |
canorm |
Further normalization, based on GCA model. Creates mri/norm.mgz. |
careg |
Computes a nonlinear transform to align with GCA atlas. Creates the file mri/transform/talairach.m3z. |
rmneck |
The neck region is removed from the NU-corrected volume mri/nu.mgz. Makes use of transform computed from prior CA Register stage. Creates the file mri/nu_noneck.mgz. |
skull_lta |
Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull. Creates the file mri/transforms/talairach_with_skull.lta. |
calabel |
Labels subcortical structures, based in GCA model. Creates the files mri/aseg.auto.mgz and mri/aseg.mgz. |
normalization2 |
Performs a second (major) intensity correction using only the brain volume as the input (so that it has to be done after the skull strip). Intensity normalization works better when the skull has been removed. Creates a new brain.mgz volume. If -noaseg flag is used, then aseg.mgz is not used by mri_normalize. |
segmentation |
Attempts to separate white matter from everything else. The input is mri/brain.mgz, and the output is mri/wm.mgz. Uses intensity, neighborhood, and smoothness constraints. This is the volume that is edited when manually fixing defects. Calls mri_segment, mri_edit_wm_with_aseg, and mri_pretess. To keep previous edits, run with -keepwmedits. If -noaseg is used, them mri_edit_wm_aseg is skipped. |
fill |
This creates the subcortical mass from which the orig surface is created. The mid brain is cut from the cerebrum, and the hemispheres are cut from each other. The left hemisphere is binarized to 255. The right hemisphere is binarized to 127. The input is mri/wm.mgz and the output is mri/filled.mgz. Calls mri_fill. If the cut fails, then seed points can be supplied (see -cc-crs, -pons-crs, -lh-crs, -rh-crs). The actual points used for the cutting planes in the corpus callosum and pons can be found in scripts/ponscc.cut.log. This is the last stage of volumetric processing. If -noaseg is used, then aseg.mgz is not used by mri_fill. |
tessellate |
This is the step where the orig surface (ie, surf/?h.orig.nofix) is created. The surface is created by covering the filled hemisphere with triangles. Runs mri_tessellate. The places where the points of the triangles meet are called vertices. Creates the file surf/?h.orig.nofix Note: the topology fixer will create the surface ?h.orig. |
smooth1 |
Calls mris_smooth. Smooth1 is the step just after tessellation |
inflate1 |
Inflation of the surf/?h.smoothwm(.nofix) surface to create surf/?h.inflated. |
qsphere |
automatic topology fixing. It is a quasi-homeomorphic spherical transformation of the inflated surface designed to localize topological defects for the subsequent automatic topology fixer. |
fix |
Finds topological defects (ie, holes in a filled hemisphere) using surf/?h.qsphere.nofix, and changes the orig surface (surf/?h.orig.nofix) to remove the defects. Changes the number of vertices. All the defects will be removed, but the user should check the orig surface in the volume to make sure that it looks appropriate. Calls mris_fix_topology. |
finalsurfs |
Creates the ?h.white and ?h.pial surfaces as well as the thickness file (?h.thickness) and curvature file (?h.curv). The white surface is created by "nudging" the orig surface so that it closely follows the white-gray intensity gradient as found in the T1 volume. The pial surface is created by expanding the white surface so that it closely follows the gray-CSF intensity gradient as found in the T1 volume. Calls mris_make_surfaces. |
smooth2 |
the step just after topology fixing. |
inflate2 |
inflate2 is the step just after topology fixing |
cortribbon |
Creates binary volume masks of the cortical ribbon, ie, each voxel is either a 1 or 0 depending upon whether it falls in the ribbon or not. Saved as ?h.ribbon.mgz. Uses mgz regardless of whether the -mgz option is used. |
sphere |
Inflates the orig surface into a sphere while minimizing metric distortion. This step is necessary in order to register the surface to the spherical atlas. (also known as the spherical morph). Calls mris_sphere. Creates surf/?h.sphere. |
surfreg |
Registers the orig surface to the spherical atlas through surf/?h.sphere. The surfaces are first coarsely registered by aligning the large scale folding patterns found in ?h.sulc and then fine tuned using the small-scale patterns as in ?h.curv. Calls mris_register. Creates surf/?h.sphere.reg. |
contrasurfreg |
Same as ipsilateral but registers to the contralateral atlas. Creates lh.rh.sphere.reg and rh.lh.sphere.reg. |
avgcurv |
Resamples the average curvature from the atlas to that of the subject. Allows the user to display activity on the surface of an individual with the folding pattern (ie, anatomy) of a group. Calls mrisp_paint. Creates surf/?h.avg_curv. |
cortparc |
Assigns a neuroanatomical label to each location on the cortical surface. Incorporates both geometric information derived from the cortical model (sulcus and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2 creates /label/?h.aparc.a2005s.annot. |
parcstats |
Runs mris_anatomical_stats to create a summary table of cortical parcellation statistics for each structure, including 1. structure name 2. number of vertices 3. total surface area (mm2) 4. total gray matter volume (mm3) 5. average cortical thickness (mm) 6. standard error of cortical thickness (mm) 7. integrated rectified mean curvature 8. integrated rectified Gaussian curvature 9. folding index 10. intrinsic curvature index. For -parcstats, the file is saved in stats/?h.aparc.stats. For -parcstats2, the file is saved in stats/?h.aparc.a2005s.stats. |
cortparc2 |
see cortparc argument |
parcstats2 |
see cortparc2 argument |
aparc2aseg |
Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. |
verbose |
print diagnostic messages |
opts |
Additional options |
Result of system
Reconstruction from Freesurfer for All Steps
recon_all( infile = NULL, outdir = NULL, subjid = NULL, verbose = TRUE, opts = "-all", ... )
recon_all( infile = NULL, outdir = NULL, subjid = NULL, verbose = TRUE, opts = "-all", ... )
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
verbose |
print diagnostic messages |
opts |
Additional options |
... |
arguments passed to |
Result of system
If you would like to restart a recon-all
run,
change opts so that opts = "-make all"
Reconstruction from Freesurfer for Step 1-5
(Motion Correction to Skull Strip), which calls -autorecon1
in recon-all
recon_con1(infile, outdir = NULL, subjid, verbose = TRUE) autorecon1(infile, outdir = NULL, subjid, verbose = TRUE) recon_con2(infile, outdir = NULL, subjid, verbose = TRUE) autorecon2(infile, outdir = NULL, subjid, verbose = TRUE) recon_con3(infile, outdir = NULL, subjid, verbose = TRUE) autorecon3(infile, outdir = NULL, subjid, verbose = TRUE)
recon_con1(infile, outdir = NULL, subjid, verbose = TRUE) autorecon1(infile, outdir = NULL, subjid, verbose = TRUE) recon_con2(infile, outdir = NULL, subjid, verbose = TRUE) autorecon2(infile, outdir = NULL, subjid, verbose = TRUE) recon_con3(infile, outdir = NULL, subjid, verbose = TRUE) autorecon3(infile, outdir = NULL, subjid, verbose = TRUE)
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
verbose |
print diagnostic messages |
Result of system
See https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all for the
steps of each autorecon1-3
.
If you set infile = NULL
, then you can omit the
-i
flag in recon-all
.
Wrapper for the recon-all
function in Freesurfer
reconner( infile = NULL, outdir = NULL, subjid = NULL, verbose = TRUE, opts = "-all", force = FALSE )
reconner( infile = NULL, outdir = NULL, subjid = NULL, verbose = TRUE, opts = "-all", force = FALSE )
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
verbose |
print diagnostic messages |
opts |
Additional options |
force |
Force running of the reconstruction |
Result of system
If you set infile = NULL
, then you can omit the
-i
flag in recon-all
Checks whether an output filename exists before a command has run, prints and runs the command, and then checks the output from the result.
run_check_fs_cmd(cmd, outfile, verbose = TRUE)
run_check_fs_cmd(cmd, outfile, verbose = TRUE)
cmd |
Command to be run |
outfile |
Output file to be produced |
verbose |
print diagnostic messages |
Invisible NULL
Sets the SUBJECTS_DIR variable in the system environment or
options("fs.subj_dir" = x)
set_fs_subj_dir(x = file.path(fs_dir(), "subjects"))
set_fs_subj_dir(x = file.path(fs_dir(), "subjects"))
x |
path to SUBJECTS_DIR defaults to |
No return value, called for side effects ('SUBJECTS_DIR' environment variable set, and 'fs.subj_dir' option set)
This function calls mri_convert
to convert a measure
from surfaces to an ASCII file and reads it in.
surf_convert(file, outfile = NULL)
surf_convert(file, outfile = NULL)
file |
(character) input filename of curvature measure |
outfile |
(character) output filename (if wanted to be saved) |
data.frame
if (have_fs()) { fname = file.path(fs_subj_dir(), "bert", "surf", "lh.thickness") out = surf_convert(fname) }
if (have_fs()) { fname = file.path(fs_subj_dir(), "bert", "surf", "lh.thickness") out = surf_convert(fname) }
Reads in a surface file from Freesurfer and converts it to a Wavefront OBJ file
surface_to_obj(infile, outfile = NULL, ...)
surface_to_obj(infile, outfile = NULL, ...)
infile |
Input surface file |
outfile |
output Wavefront OBJ file. If |
... |
additional arguments to pass to
|
Character filename of output file
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") res = surface_to_obj(infile = infile) }
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") res = surface_to_obj(infile = infile) }
Reads in a surface file from Freesurfer and converts it into triangles
surface_to_triangles(infile, ...)
surface_to_triangles(infile, ...)
infile |
Input surface file |
... |
additional arguments to pass to
|
Matrix of triangles with the number of rows equal to the number of faces (not the triplets - total faces)
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") right_triangles = surface_to_triangles(infile = infile) infile = file.path(fs_subj_dir(), "bert", "surf", "lh.pial") left_triangles = surface_to_triangles(infile = infile) if (requireNamespace("rgl", quietly = TRUE)) { rgl::open3d() rgl::triangles3d(right_triangles, color = rainbow(nrow(right_triangles))) rgl::triangles3d(left_triangles, color = rainbow(nrow(left_triangles))) } infile = file.path(fs_subj_dir(), "bert", "surf", "rh.inflated") right_triangles = surface_to_triangles(infile = infile) infile = file.path(fs_subj_dir(), "bert", "surf", "lh.inflated") left_triangles = surface_to_triangles(infile = infile) if (requireNamespace("rgl", quietly = TRUE)) { rgl::open3d() rgl::triangles3d(left_triangles, color = rainbow(nrow(left_triangles))) rgl::triangles3d(right_triangles, color = rainbow(nrow(right_triangles))) } }
if (have_fs()) { infile = file.path(fs_subj_dir(), "bert", "surf", "rh.pial") right_triangles = surface_to_triangles(infile = infile) infile = file.path(fs_subj_dir(), "bert", "surf", "lh.pial") left_triangles = surface_to_triangles(infile = infile) if (requireNamespace("rgl", quietly = TRUE)) { rgl::open3d() rgl::triangles3d(right_triangles, color = rainbow(nrow(right_triangles))) rgl::triangles3d(left_triangles, color = rainbow(nrow(left_triangles))) } infile = file.path(fs_subj_dir(), "bert", "surf", "rh.inflated") right_triangles = surface_to_triangles(infile = infile) infile = file.path(fs_subj_dir(), "bert", "surf", "lh.inflated") left_triangles = surface_to_triangles(infile = infile) if (requireNamespace("rgl", quietly = TRUE)) { rgl::open3d() rgl::triangles3d(left_triangles, color = rainbow(nrow(left_triangles))) rgl::triangles3d(right_triangles, color = rainbow(nrow(right_triangles))) } }
Wrapper for the trac-all
function in Freesurfer
for All Steps
trac_all(infile, outdir = NULL, subjid, verbose = TRUE, opts = "")
trac_all(infile, outdir = NULL, subjid, verbose = TRUE, opts = "")
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
verbose |
print diagnostic messages |
opts |
Additional options |
Result of system
Reconstruction from Freesurfer for Preprocessing, Bedpost, and Path reconstruction
trac_prep(infile, outdir = NULL, subjid, verbose = TRUE) trac_bedpost(infile, outdir = NULL, subjid, verbose = TRUE) trac_path(infile, outdir = NULL, subjid, verbose = TRUE)
trac_prep(infile, outdir = NULL, subjid, verbose = TRUE) trac_bedpost(infile, outdir = NULL, subjid, verbose = TRUE) trac_path(infile, outdir = NULL, subjid, verbose = TRUE)
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id |
verbose |
print diagnostic messages |
Result of system
Wrapper for the trac-all
function in Freesurfer
tracker(infile, outdir = NULL, subjid, verbose = TRUE, opts = "")
tracker(infile, outdir = NULL, subjid, verbose = TRUE, opts = "")
infile |
Input filename (dcm or nii) |
outdir |
Output directory |
subjid |
subject id, if NULL, the basename of the infile will be used |
verbose |
print diagnostic messages |
opts |
Additional options |
Result of system