Skip to content

Commit 23fb760

Browse files
lafayecran-robot
lafaye
authored and
cran-robot
committedMay 14, 2018
version 1.1-17
·
1.1-241.1-17
1 parent e1923d8 commit 23fb760

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

44 files changed

+1770
-1648
lines changed
 

‎DESCRIPTION

+10-13
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,14 @@
11
Package: AnalyzeFMRI
2-
Version: 1.1-16
3-
Date: 2013-03-19
4-
Title: Functions for analysis of fMRI datasets stored in the ANALYZE or
5-
NIFTI format.
6-
Author: P Lafaye de Micheaux <lafaye@dms.umontreal.ca>, J L Marchini
7-
<marchini@stats.ox.ac.uk>
8-
Maintainer: P Lafaye de Micheaux <lafaye@dms.umontreal.ca>
9-
Depends: tcltk, R.matlab, fastICA
10-
Description: Functions for I/O, visualisation and analysis of
11-
functional Magnetic Resonance Imaging (fMRI) datasets stored in
12-
the ANALYZE or NIFTI format.
2+
Version: 1.1-17
3+
Date: 2018-05-09
4+
Title: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
5+
NIFTI Format
6+
Author: P Lafaye de Micheaux <lafaye@unsw.edu.au>, J L Marchini <marchini@stats.ox.ac.uk>
7+
Maintainer: Pierre Lafaye de Micheaux <lafaye@unsw.edu.au>
8+
Depends: R (>= 2.13.0), R.matlab, fastICA, tcltk, tkrplot
9+
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format. Note that the latest version of XQuartz seems to be necessary under MacOS.
1310
License: GPL (>= 2)
14-
Packaged: 2013-03-19 12:41:20 UTC; lafaye
11+
Packaged: 2018-05-14 00:33:10 UTC; lafaye
1512
NeedsCompilation: yes
1613
Repository: CRAN
17-
Date/Publication: 2013-03-19 15:38:10
14+
Date/Publication: 2018-05-14 05:33:04 UTC

‎INDEX

+92-79
Original file line numberDiff line numberDiff line change
@@ -1,93 +1,98 @@
1-
analyze2nifti Create a NIFTI file from an Analyze file
2-
centering centering
1+
analyze2nifti Create a NIFTI file from an Analyze file
2+
3+
centering Center the data in the two dimensions
4+
35
cluster.threshold Cluster threshold an array.
46
cov.est Estimates the covariance between neighbouring
57
voxels
6-
diminfo2fps diminfo2fps
8+
9+
diminfo2fps dim.info field to freq.dim, phase.dim and slice.dim fields
10+
711
EC.3D Expected Euler Characteristic for a 3D Random
812
Field
9-
eigenvalues eigenvalues
10-
f.analyze.file.summary
11-
prints summary of .img file contents
12-
f.analyzeFMRI.gui starts AnalyzeFMRI GUI
13-
f.basic.hdr.list.create
14-
creates basic .hdr list in ANALYZE format
15-
f.basic.hdr.nifti.list.create
16-
creates basic .hdr list in NIFTI format
17-
f.complete.hdr.nifti.list.create
18-
creates complete .hdr list in NIFTI format
13+
14+
eigenvalues Computes the eigenvalues of a centered and reduced data matrix
15+
16+
fourDto2D Transform a 4D image into a 2D image matrix
17+
fps2diminfo freq.dim, phase.dim and slice.dim fields into dim.info field
18+
19+
f.analyze.file.summary Prints summary of ANALYZE .img file contents
20+
f.nifti.file.summary Prints summary of NIFTI .img file contents
21+
22+
f.analyzeFMRI.gui Starts AnalyzeFMRI GUI
23+
f.basic.hdr.list.create Creates basic ANALYZE .hdr list
24+
f.basic.hdr.nifti.list.create
25+
Creates basic NIFTI .hdr list
26+
f.complete.hdr.nifti.list.create
27+
Creates complete NIFTI .hdr list
28+
1929
f.ica.fmri Applies Spatial ICA (Independent Component
2030
Analysis) to fMRI datasets
21-
f.ica.fmri.gui tcltk GUI to apply ICA to fMRI datasets
22-
f.icast.fmri Applies Spatial or Temporal ICA (Independent
23-
Component Analysis) to fMRI NIFTI datasets
24-
f.icast.fmri.gui tcltk GUI to apply Spatial or Temporal ICA to
25-
fMRI NIFTI datasets
26-
f.nifti.file.summary prints summary of .img file contents
31+
f.icast.fmri Applies Spatial or Temporal ICA (Independent Component
32+
Analysis) to fMRI NIFTI datasets
33+
f.ica.fmri.gui tcltk GUI to apply Spatial ICA to fMRI Analyze datasets
34+
f.icast.fmri.gui tcltk GUI to apply Spatial or Temporal ICA to NIFTI fMRI datasets
2735
f.plot.ica.fmri Plots a specified component from the output of
2836
f.ica.fmri
2937
f.plot.ica.fmri.jpg Plot the components of the ouput of f.ica.fmri
3038
to a series of jpeg files
31-
f.plot.volume.gui tcltk GUI to display FMRI or MRI images
32-
f.read.analyze.header read Analyze header file
33-
f.read.analyze.slice read one slice from a .img file
39+
f.read.analyze.header Read Analyze header file
40+
f.read.analyze.slice Read one slice from an ANALYZE .img file
41+
f.read.nifti.slice Read one slice from a NIFTI .img file
3442
f.read.analyze.slice.at.all.timepoints
35-
reads a slice at all time points from a .img
36-
file
37-
f.read.analyze.tpt Read in a volume at one time point
38-
f.read.analyze.ts read in one voxel time series
39-
f.read.analyze.volume read whole .img file
40-
f.read.header read ANALYZE or NIFTI header file
41-
f.read.nifti.header read Nifti header file
42-
f.read.nifti.slice read one slice from a .img or .nii file in
43-
NIFTI format
43+
Reads a slice at all time points from an ANALYZE .img file
4444
f.read.nifti.slice.at.all.timepoints
45-
reads a slice at all time points from a NIFTI
46-
.img or .nii file
47-
f.read.nifti.tpt Read in a volume at one time point
48-
f.read.nifti.ts read in one voxel time series
49-
f.read.nifti.volume read whole image file
50-
f.read.volume read whole image file
51-
f.spectral.summary plots graphical summary of spectral properties
52-
of an fMRI dataset
53-
f.spectral.summary.nifti
54-
plots graphical summary of spectral properties
55-
of an fMRI dataset
56-
f.write.analyze writes an array to a .img/.hdr pair in ANALYZE
57-
format
45+
Reads a slice at all time points from a NIFTI .img file
46+
f.read.analyze.tpt Read in a volume at one time point from an ANALYZE file
47+
f.read.nifti.tpt Read in a volume at one time point from a NIFTI file
48+
f.read.analyze.ts Read in one voxel time series from an ANALYZE .img file
49+
f.read.nifti.ts Read in one voxel time series from a NIFTI .img or .nii file
50+
f.read.analyze.volume Read whole ANALYZE .img or .nii file
51+
f.read.nifti.volume Read whole NIFTI image file
52+
f.read.volume Read whole ANALYZE or NIFTI image file (autodetecting the format)
53+
f.read.nifti.header Read Nifti header file
54+
f.read.header Read Analyze and Nifti header files
55+
f.spectral.summary Plots graphical summary of spectral properties
56+
of an ANALYZE fMRI dataset
57+
f.spectral.summary.nifti
58+
Plots graphical summary of spectral properties
59+
of a NIFTI fMRI dataset
60+
f.write.analyze Writes an array to an ANALYZE .img/.hdr pair
61+
f.write.nifti Writes an array to a NIFTI .img/.hdr pair
62+
5863
f.write.array.to.img.2bytes
59-
write array of 2 byte integers
64+
Write array of 2 byte integers
6065
f.write.array.to.img.8bit
61-
write array of 1 byte integers
66+
Write array of 1 byte integers
6267
f.write.array.to.img.float
63-
write array of 4 byte floats
64-
f.write.list.to.hdr writes a .hdr file in ANALYZE format
65-
f.write.list.to.hdr.nifti
66-
writes a .hdr file in NITI format
67-
f.write.nifti writes an array to a .img/.hdr pair in NIFTI
68-
format or to a .nii file
68+
Write array of 4 byte floats
69+
6970
f.write.nii.array.to.img.2bytes
70-
write array of 2 byte integers and add at the
71-
begining of the file the NIFTI header part
71+
Write array of 2 byte integers and add at the begining of the file the NIFTI header part
7272
f.write.nii.array.to.img.8bit
73-
write array of 1 byte integers and add at the
74-
begining of the file the NIFTI header part
73+
Write array of 1 byte integers and add at the begining of the file the NIFTI header part
7574
f.write.nii.array.to.img.float
76-
write array of 4 byte floats and add at the
77-
begining of the file the NIFTI header part
78-
fourDto2D fourDto2D
79-
fps2diminfo fps2diminfo
75+
Write array of 4 byte floats and add at the begining of the file the NIFTI header part
76+
77+
78+
f.write.list.to.hdr Writes an ANALYZE .hdr file
79+
f.write.list.to.hdr.nifti
80+
Writes a NIFTI .hdr file
81+
8082
GaussSmoothArray Spatially smooth an array with Gaussian kernel.
8183
GaussSmoothKernel Calculates a discrete Gaussian smoothing
8284
kernel.
83-
ICAspat ICAspat
84-
ICAtemp ICAtemp
85-
ijk2xyz ijk2xyz
86-
magicfield Get magicfield from the header of an image file
87-
mat34.to.TRSZ Affine 4x4 (or 3x4) matrix to Translation,
88-
Rotation, Shear and Scale
89-
mat34.to.TZSR Affine 4x4 (or 3x4) matrix to Translation,
90-
Scale, Shear and Rotation
85+
86+
ICAspat Performs a spatial ICA
87+
ICAtemp Performs a temporal ICA
88+
89+
ijk2xyz Maps from data coordinates (e.g. column i, row j, slice k), into some real world (x,y,z) positions in space.
90+
91+
magicfield Get magic field from the header of an image file
92+
93+
mat34.to.TRSZ Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear and Scale
94+
mat34.to.TZSR Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotation
95+
9196
model.2.cov.func Calculates covariance from Hartvig Model 2
9297
model.2.est.gamma Estimate gamma for Model 2 of Hartvig and
9398
Jensen (2000)
@@ -105,22 +110,30 @@ N2G.Region N2G Normal component interval
105110
N2G.Spatial.Mixture fMRI Spatial Mixture Modelling
106111
N2G.Transform Transform parameters of N2G model so as to lie
107112
on the real line.
108-
nifti.quatern.to.mat44
109-
Quaternion (etc..) to affine 4x4 matrix
113+
nifti.quatern.to.mat44 Quaternion (etc..) to affine 4x4 matrix
110114
NonLinearSmoothArray Non-linear spatial smmothing of 3D and 4D
111115
arrays.
112-
Q2R Quaternion to rotation
113-
R2Q Rotation to quaternion
114-
reduction reduction
116+
117+
orientation Returns storage mode (Radiological or Neurological)
118+
119+
Q2R Generate a rotation matrix from a quaternion
120+
R2Q Convert from rotation matrix to quaternion form
121+
122+
reduction Reduces the data in the row or col dimension
123+
115124
Sim.3D.GammaRF Simulate Gamma distributed Random Field
116125
Sim.3D.GRF Simulate a GRF
117126
SmoothEst Estimate the variance-covariance matrix of a
118127
Gaussian random field
119-
st2xyzt st2xyzt
120-
threeDto4D threeDto4D
128+
129+
st2xyzt Encode space and time dimensions fields into the xyzt.units field
130+
131+
threeDto4D Read tm functionnal images and concatenate them to obtain one (hdr/img pair) 4D image file (Analyze or Nifti format) which is written on disk
132+
121133
Threshold.Bonferroni Calculates Bonferroni Threshold
122134
Threshold.FDR False Discovery Rate (FDR) Threshold
123-
Threshold.RF Random Field Theory Thersholds.
124-
twoDto4D twoDto4D
125-
xyz2ijk xyz2ijk
126-
xyzt2st xyzt2st
135+
Threshold.RF Random Field Theory Thresholds.
136+
137+
twoDto4D Transform a 2D matrix of size tm x vm containing images in each row into a 4D array image
138+
139+
xyzt2st Extract space and time dimensions fields from xyzt.units field

0 commit comments

Comments
 (0)
Please sign in to comment.