From 20ced5e0d4cd4965dc626b0881622e0016ecc5d7 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Tue, 11 Jun 2019 15:25:38 +0000
Subject: [PATCH] This commit was manufactured by cvs2svn to create tag
'FSL6-0-2'.
Sprout from master 2019-06-11 15:25:37 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'read4D to avoid calling legacy read'
Cherrypick from master 2009-03-31 10:49:37 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'fixed copyrights':
fsl2ascii.cc
Cherrypick from fsl-5_branch 2014-02-12 12:05:15 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'Changes for new utils parser':
fslcc.cc
Delete:
avwfixfloat.cc
doc/index.html
fslcheck.cc
fslcorrecthd.cc
fsldecorr4d.cc
fslfromascii.cc
tests/avw2ascii_test.sh
tests/avwcc_test.sh
tests/avwcpgeom_test.sh
tests/avwcreatehd_test.sh
tests/avwhd_test.sh
tests/avwinterleave_test.sh
tests/avwmaths_test.sh
tests/avwmerge_test.sh
tests/avwnvols_test.sh
tests/avwroi_test.sh
tests/avwsplit_test.sh
tests/fslswapdim_test.sh
tests/header.xml
tests/run_alltests.sh
---
avwfixfloat.cc | 128 ----------
doc/index.html | 465 ------------------------------------
fsl2ascii.cc | 8 +-
fslcc.cc | 7 +-
fslcheck.cc | 140 -----------
fslcorrecthd.cc | 94 --------
fsldecorr4d.cc | 325 -------------------------
fslfromascii.cc | 37 ---
tests/avw2ascii_test.sh | 33 ---
tests/avwcc_test.sh | 38 ---
tests/avwcpgeom_test.sh | 97 --------
tests/avwcreatehd_test.sh | 35 ---
tests/avwhd_test.sh | 61 -----
tests/avwinterleave_test.sh | 50 ----
tests/avwmaths_test.sh | 389 ------------------------------
tests/avwmerge_test.sh | 48 ----
tests/avwnvols_test.sh | 31 ---
tests/avwroi_test.sh | 77 ------
tests/avwsplit_test.sh | 28 ---
tests/fslswapdim_test.sh | 56 -----
tests/header.xml | 28 ---
tests/run_alltests.sh | 36 ---
22 files changed, 8 insertions(+), 2203 deletions(-)
delete mode 100644 avwfixfloat.cc
delete mode 100644 doc/index.html
delete mode 100644 fslcheck.cc
delete mode 100755 fslcorrecthd.cc
delete mode 100644 fsldecorr4d.cc
delete mode 100755 fslfromascii.cc
delete mode 100755 tests/avw2ascii_test.sh
delete mode 100755 tests/avwcc_test.sh
delete mode 100755 tests/avwcpgeom_test.sh
delete mode 100755 tests/avwcreatehd_test.sh
delete mode 100755 tests/avwhd_test.sh
delete mode 100755 tests/avwinterleave_test.sh
delete mode 100755 tests/avwmaths_test.sh
delete mode 100755 tests/avwmerge_test.sh
delete mode 100755 tests/avwnvols_test.sh
delete mode 100755 tests/avwroi_test.sh
delete mode 100755 tests/avwsplit_test.sh
delete mode 100755 tests/fslswapdim_test.sh
delete mode 100644 tests/header.xml
delete mode 100755 tests/run_alltests.sh
diff --git a/avwfixfloat.cc b/avwfixfloat.cc
deleted file mode 100644
index 81744e8..0000000
--- a/avwfixfloat.cc
+++ /dev/null
@@ -1,128 +0,0 @@
-/* avwfixfloat.cc
-
- Mark Jenkinson, FMRIB Image Analysis Group
-
- Copyright (C) 2003 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#include <math.h>
-#include <iostream>
-#include <string>
-#include "newimage/newimageall.h"
-
-using namespace NEWIMAGE;
-
-void dump_float(float *fptr) {
- char *cptr;
- cptr = (char *) fptr;
- cerr << (int) *cptr << " , " << (int) *(cptr+1) << " , "
- << (int) *(cptr+2) << " , " << (int) *(cptr+3) << " ";
-}
-
-
-// void check_volume(const volume4D<float>& vol1) {
-// long int count=0;
-// float val, sum=0.0;
-// for (int t=0; t<vol1.tsize(); t++) {
-// for (int z=0; z<vol1.zsize(); z++) {
-// for (int y=0; y<vol1.ysize(); y++) {
-// for (int x=0; x<vol1.xsize(); x++) {
-// count++;
-// val = vol1(x,y,z,t);
-// sum += val;
-// }
-// }
-// }
-// }
-// }
-
-
-int main(int argc, char *argv[])
-{
-
- if (argc<2) {
- cerr << "Usage: " << argv[0] << " <input_volume> [output_volume] [-v]"
- << endl;
- return -1;
- }
-
- string outname="";
- bool verbose = false;
- if (argc>=3) {
- outname = argv[2];
- if (outname == "-v" ) {
- verbose = true;
- outname = "";
- }
- }
-
- string optarg;
- if (argc>=4) {
- optarg = argv[3];
- if (optarg=="-v") {
- verbose = true;
- }
- }
-
- volume4D<float> vol1;
- volumeinfo vinfo;
- read_volume4D(vol1,argv[1],vinfo);
- long int count=0, badcount=0, nancount=0;
- float val, sum=0;
- for (int t=0; t<vol1.tsize(); t++) {
- for (int z=0; z<vol1.zsize(); z++) {
- for (int y=0; y<vol1.ysize(); y++) {
- for (int x=0; x<vol1.xsize(); x++) {
- count++;
- if (verbose) {
- cerr << "x,y,z,t = " << x <<","<<y<<","<<z<<","<<t<<" : ";
- dump_float(&vol1(x,y,z,t));
- }
- char *cptr;
- cptr = (char *) &(vol1(x,y,z,t));
- int ival0 = (int) *cptr;
- int ival1 = (int) *(cptr+1);
- int ival2 = (int) *(cptr+2);
- int ival3 = (int) *(cptr+3);
-
- if ( ( (ival3==0) && ( (ival0!=0) || (ival1!=0) || (ival2!=0) ) ) ||
- (ival3<-125) )
- {
- badcount++;
- if (verbose) {
- cerr << "BAD VALUE DETECTED - fixing it" << endl;
- dump_float((float *) cptr); cerr << endl;
- }
- *(cptr+0) = 0;
- *(cptr+1) = 0;
- *(cptr+2) = 0;
- *(cptr+3) = 0;
- }
-
- if (! finite(vol1(x,y,z,t))) {
- nancount++;
- vol1(x,y,z,t) = 0.0;
- }
-
- val = vol1(x,y,z,t);
- sum += val;
- if (verbose) cerr << " :: " << vol1(x,y,z,t) << " :: " << endl;
- }
- if (verbose) cerr << y << ",";
- }
- if (verbose) cerr << endl << "Z = " << z << endl;
- }
- if (verbose) cerr << endl << "T = " << t << endl;
- }
- cout << "Successfully parsed volume" << endl;
- cout << "Found " << badcount << " invalid elements out of " << count << endl;
- cout << "Found " << nancount << " non-finite elements out of " << count
- << endl;
- if (verbose) print_volume_info(vol1,"Volume");
- if (outname.size()>0) {
- cout << "Saving volume ... " << endl;
- save_volume4D(vol1,outname,vinfo);
- cout << "done" << endl;
- }
-}
diff --git a/doc/index.html b/doc/index.html
deleted file mode 100644
index 00a63c7..0000000
--- a/doc/index.html
+++ /dev/null
@@ -1,465 +0,0 @@
-<HTML><HEAD><link REL="stylesheet" TYPE="text/css" href="../fsl.css"><TITLE>FSLUTILS DOCS</TITLE></HEAD><BODY><hr><TABLE BORDER=0 WIDTH="100%"><TR><TD ALIGN=CENTER><H1>
-FSLUTILS
-</H1>
-Miscellaneous FSL Image Utilities
-<TD ALIGN=RIGHT><a href="../index.html"><IMG BORDER=0 SRC="../images/fsl-logo.jpg"></a></TR></TABLE><HR>
-
-<P>FSLUTILS is a set of useful command-line utilities which allow the
-conversion, processing etc. of Analyze and Nifti format data sets.
-Many of them work on both 3D and 4D data. For each of these programs,
-<i>type just the program name to get the usage help</i>.
-
-
-<p>The different FSLUTILS programs are:
-<UL>
-
-<LI><b>fsl2ascii</b> - convert image files to ASCII text file (or files if
-data is 4D).
-
-<br><br><LI><b>fslcc</b> - run cross-correlations between every volume in
-one 4D data set with every volume in another (for investigating
-similarities in ICA outputs).
-
-<br><br><LI><b>fslchfiletype</b> - used to change the file type of
-an image (e.g. from ANALYZE_GZ to NIFTI). The first argument is
-the desired file type (one of ANALYZE, ANALYZE_GZ, NIFTI, NIFTI_GZ,
-NIFTI_PAIR, NIFTI_PAIR_GZ) and the second is the input file. If
-no third argument is given then the input file is converted in place.
-This in place conversion removes the original files: e.g. for an
-Analyze file called stdimg then
-<kbd>fslchfiletype NIFTI_GZ stdimg</kbd> would replace stdimg.hdr and
-stdimg.img with stdimg.nii.gz. Note that having multiple copies of
-an image with the same basename and different filetypes (e.g. stdimg.nii.gz
-and stdimg.hdr and stdimg.img) creates many problems for determining
-what images to read, and in general will cause FSL programs to stop.
-
-<br><br><a name="fslcomplex"></a><LI><b>fslcomplex</b> - a utility that allows 3D or 4D complex
-image files to be split or constructed from corresponding real
-components (either Cartesian or polar). The initial flag indicates
-what kind of processing is done. In addition, two optional arguments
-at the end specify the first and last 3D volumes to be processed when
-the input is 4D (default is to do all volumes).
-
-<br><br><LI><b>fslcpgeom</b> - copy certain parts of the header
-information (image
-dimensions, voxel dimensions, voxel dimensions units string, image
-orientation/origin or qform/sform info) from one image to another.
-Note that only copies from Analyze to Analyze or Nifti to Nifti
-will work properly. Copying from different files will result in
-loss of information or potentially incorrect settings.
-
-<br><br><LI><b>fslcreatehd</b> - creates a new image header along with
-a zero intensity data image. There are two forms of input: one takes
-a list of minimal information on the command line, the other takes in
-an xml-style file, as written by <kbd>fslhd -x</kbd>. The information
-required in the first version is: x/y/z/tsize for image dimensions,
-x/y/zvoxsize for voxel dimensions (eg in mm), tr in seconds for time
-between volumes (for 3D data set to 0), x/y/zorigin for voxel
-co-ordinate origin (eg for standard space - otherwise leave as 0 0 0),
-datatype for the voxel data type (the commonest are: 1=binary,
-2=unsigned char, 4=signed short, 8=signed int, 16=float). Note that
-this is <b><i>different</i></b> from the previous versions in that an
-entire image is created, and will <b><i>overwrite</i></b> any
-<kbd>.img</kbd> file contents of the same image name.
-
-<br><br><LI><b>fsledithd</b> - allows the header information in
-and image to be edited in a text-based xml-style format (like the
-output of <kbd>fslhd -x</kbd> but with redundant fields removed
-and some help text provided). Note that
-the default text editor used is nano, but other editors can be
-specified by the second argument.
-
-<br><br><LI><b>fslfft</b> - outputs the Fast-Fourier Transform (or inverse)
-for a complex input volume.
-
-<br><br><LI><b>fslhd</b> - report every field of an Analyze or Nifti
-header (note that the fields are different although some are common,
-e.g. pixdims). The option "-x" produces an xml-style output which can
-be used in conjunction with <kbd>fslcreatehd</kbd>. The reported
-values are those used internally in FSL programs and are sometimes
-different from the raw values stored in the file to avoid incorrect
-settings (e.g. dimN has a minimum value of 1, not 0).
-
-<br><br><LI><b>fslinfo</b> - report a basic subset of an Analyze or
-Nifti header.
-
-<br><br><LI><b>fslinterleave</b> - interleave two inputs to form a
-combined image.
-
-<br><br><LI><b>fslmaths</b> - simple but powerful program to allow
-mathematical manipulation of images. Now includes spatial and
-temporal filtering, statistic conversion (e.g. z to p-values),
-diffusion tensor decomposition, and TFCE calculation.
-
-<br><br><LI><b>fslmeants</b> - output the average timeseries of a set of voxels, or the individual time series for each of these voxels.
-
-<br><br><LI><b>fslmerge</b> - concatenate image files into a single
-output. This concatenation can be in time, or in X, Y or Z. All image
-dimensions (except for the one being concatenated over) must be the
-same in all input images. For example, this can be used to take
-multiple 3D files (eg as output by SPM) and create a single 4D image
-file.
-
-<br><br><LI><b>fslnvols</b> - report how many time points are in the
-input 4D data set.
-
-<br><br><LI><b>fslpspec</b> - outputs the spectral power density of an
-input 4D data set.
-
-<br><br><LI><b>fslroi</b> - extract region of interest (ROI) from an
-image. You can a) take a 3D ROI from a 3D data set (or if it is 4D,
-the same ROI is taken from each time point and a new 4D data set is
-created), b) extract just some time points from a 4D data set, or c)
-control time and space limits to the ROI. Note that the arguments are
-minimum index and <i>size</i> (not maximum index). So to extract
-voxels 10 to 12 inclusive you would specify 10 and 3 (not 10 and 12).
-
-<br><br><LI><b>fslslice</b> - split a 3D file into lots of 2D files (along z-axis).
-
-<br><br><LI><b>fslsplit</b> - split a 4D file into lots of 3D files
-(eg for inputting to SPM).
-
-<br><br><LI><b>fslstats</b> - report certain summary statistics for an
-input 3D/4D image. Of particular value is the "robust intensity range"
-which calculates values similar to the 2% and 98% percentiles, but
-ensuring that the majority of the intensity range is captured, even
-for binary images. In addition, it can take an aribitrary mask as
-input so that statistics are only calculated within the mask and can
-also generate histogram data.
-
-<br><br><LI><b>fslval</b> - report a particular parameter (given a
-particular keyword eg "dim4") from an image header. To see the list of
-keywords run <kbd>fslhd</kbd> on the header and look at the first column.
-
-</ul>
-
-<hr>
-<h2>Orientation-related Utilities</h2>
-
-<p> Orientation, labelling and getting left and right correct are
-important but often confusing issues. You should always look at your
-data and check if the labels in FSLView are correct. <b><i>No further
-analysis should ever be done if the labels in FSLView are incorrect or
-missing.</i></b> If your labels are fine then you probably will not
-need to use any other these tools, although
-<code>fslreorient2std</code> may be useful. If not, then you will need
-to read on. We have tried to simplify the usage of the tools for
-common tasks involving orientation issues, although still providing
-flexible and powerful tools for the expert user.
-
-<p>
-<b>Common problems</b>
-<br>We describe here the most common problems and how to solve
-them. If you have a different problem then you will need to work
-with the advanced tools described later (and read the information on
-NIfTI orientation).
-<ol>
- <li> <b>The labels in FSLView are wrong or missing</b>
- <br> This is <i>very serious</i> and needs to be fixed before doing
- any analysis at all. Ideally it should be fixed by using a
- tool that creates a correct NIfTI file. There are numerous
- converters from DICOM to NIfTI -- for recommendations, see the
- <a href="http://www.fmrib.ox.ac.uk/fslfaq">FSL FAQ</a>.
- A correct converter should store the correct information in the
- NIfTI file so that the labels are correct when viewed in FSLView.
- If you have tried many converters and still cannot get the images
- converted correctly then you will need to use the advanced tools,
- <code>fslswapdim</code> and <code>fslorient</code>, to fix the
- problem (more info below).
- <li> <b>The labels in FSLView are correct but the image is oriented
- "wrongly"</b>
- <br> By default FSLView shows the image in the way that the scanner
- acquired it, so that sagittal, coronal and axial scans look very
- different. Hence this is not really "wrong" - just how FSLView
- chooses to display the images. If you do not want this but want to
- see the image in the same orientation as the standard templates
- (MNI152) then you can run the tool <code>fslreorient2std</code>
- which is designed for just this task. However, make sure that the
- labels are correct in FSLView to start with, as this tool only works if they are correct.
-</ol>
-
-<!---
-The following utilities allow you to report and modify the
-orientation information in NIFTI files (and ANALYZE to some extent).
-For more information about orientation and the NIFTI format see
-the <a href="http://www.fmrib.ox.ac.uk/fslfaq">FSL FAQ</a>.
-!--->
-
-<p>
-<b>Tools</b>
-<ul>
- <LI><b>fslreorient2std</b> - this is a simple tool designed to
- reorient an image to match the orientation of the standard template
- images (MNI152) so that they appear "the same way around" in
- FSLView. It requires that the image labels are correct in FSLView
- before this is run. It is also not a registration tool, so it will
- not align the image to standard space, it will only apply 90,
- 180 or 270 degree rotations about the different axes as necessary to
- get the labels in the same position as the standard template.
-
- <br><br><LI><b>fslorient</b> - this is an advanced tool that reports
-or sets the orientation information in a file. Note that only in
-NIfTI files can the orientation be changed - Analyze files are
-<i>always treated as "radiological"</i> (meaning that they could
-be simply rotated into the same alignment as the <code>MNI152</code> standard
-images - equivalent to the appropriate <i>sform</i> or <i>qform</i> in
-a NIfTI file having a negative determinant).
-
-<p>In nifti files it is possible to independently report or modify
-the <i>qform</i> or <i>sform</i> fields (see below for background
- information on NIfTI orientation). However, the FSL4.1 output
-routines will try to keep
-<i>qform and sform matrices the same</i> whenever one would otherwise
-be unset. Therefore it is not possible, for instance, to delete only
-the qform, as if the sform is set then doing this will result in the
-qform being set equal (as close as possible) to the sform. This is
-currently done to aid interoperability with other packages. However, if both
-qform and sform are given different values then these are
-preserved by the output routines.
-
-<p>This command does not change the data storage at all - only the
-orientation information in the header and so should be used with great
- caution. Only modify header information if you understand the
- information about the NIfTI orientation given below or are following
- (exactly) a set of steps prescribed by someone who does.
-
-<p>The option <code>-deleteorient</code> is useful for the first stage
-of correcting orientation/label information in images where the
-conversion to NIfTI does not provide the correction information. Note
-that the first, and by far the best, solution to this problem is to
-find a method of converting the images to NIfTI in a way that
-correctly stores the information (see above) but if this really is
-not possible then a combination of <code>fslorient</code> and
-<code>fslswapdim</code> can be used to fix it (see below).
-
-<br><br><LI><b>fslswapdim</b> - this is an advanced tool that
-re-orders the data storage to permit changes between axial, sagittal
-and coronal slicing. When used in this mode the same left-right
-convention (also called coordinate handedness or
-radiological/neurological convention) will be maintained <i>as long as
-no warning is printed</i>.
-
-<p>
-The new orientation of the data is specified by selecting what the new
-axes should represent. This can either be done in terms of the old
-axes (<kbd>x y z -x -y -z</kbd>) or in terms of anatomical labels
-<i>when this information is available</i> (in a nifti image where
-either the sform or qform code is non-zero). The anatomical labels
-are RL LR AP PA SI IS. Note that the anatomical label version will not
-allow the left-right convention to be changed.
-
-<p>
-Ordinarily <kbd>fslswapdim</kbd> will change the orientation
-information in the header as well as reordering the data. This is so
-that the anatomical labels stay attached to the same parts of the
-image and not fixed to the voxel coordinates. Hence, reordering a
-coronal image to axial slicing should keep the labels correctly
-attached to the relevant parts of the image, as long as they were
-correct initially. If the initial labels are incorrect (see the
-labels in <kbd>fslview</kbd>) then <kbd>fslorient</kbd> needs to be
-used in conjunction with <kbd>fslswapdim</kbd> in order to correct
-this.
-
-<p> When <kbd>fslswapdim</kbd> is given arguments that will change the
-left-right orientation it will issue a warning that the left-right
-orientation is being flipped. It will also try to modify the
-orientation information in the header (only when either the sform or
-qform code is non-zero), but <i>not</i> in a way that swaps this
-left-right orientation in the header. Hence there is a net change in
-orientation as the data is swapped while the header is not. If the
-swap occurs on the x-axis then nothing is done to the header at all.
-Otherwise, the axis which is being swapped, together with the x-axis,
-have their orientation changed. In this way the handedness of the
-header is preserved, the labels associated with the y-axis and z-axis
-follow the image change, but the x-axis labels do not. It is
-recommended that if a left-right swap in storage is desired (and this
-should only be done if the reconstruction is initially incorrect, and
-cannot be fixed by finding any better conversion method) then the
-arguments <kbd>-x y z</kbd> should be used as this is the simplest
-form of swapping since it only affects the x-axis data and no labels
-or header information is changed.
-
-</UL>
-
-<p>
-<b>Serious (uncommon) problems</b>
-<br>
-<ol>
- <li><b>The labels in FSLView are wrong or missing and no conversion
- to NIfTI can fix this</b>
- <br>If this really cannot be fixed at the conversion stage, then it
- is possible to fix by the follow (only to be attempted after reading
- the following section on background information on NIfTI
- orientation):
- <br> <code>fslorient -deleteorient <i>imagename</i></code>
- <br> <code>fslswapdim <i>imagename</i> <i>a b c</i> <i>imagename</i></code>
- <br> <code>fslorient -setqformcode 1 <i>imagename</i></code>
- <br> where <i>a b c</i> need to be chosen, usually by trial and
- error, so that the image after this is in the same orientation (as
- viewed in FSLView) as the MNI152 images. However, unless you have
- some way of telling left from right in the image (e.g. by a vitamin
- capsule or clearly known structural asymmetry) this method can
- easily result in an incorrect left-right labelling and so should not
- be attempted.
-</ol>
-
-<p>
-<b>Background information on NIfTI Orientation</b>
-<br>
-
-This section is purely optional but is extremely useful to understand
-if you are working with any of the advanced tools, have unusual
-problems, or are just plain interested.
-
-<p>
-
-The NIfTI standard is confusing for many people on the issue of
-orientation, largely because it is intrinsically a confusing issue.
-It is complicated because the intensity data is stored on disk as a
-list of numbers - there is no concept of spatial or anatomical
-location with these numbers, and so information and standard
-conventions are used to associate spatial and anatomical location
-information with these numbers.
-
-<p>
-
-To start with, voxel coordinates are associated with the numbers (intensity values), such
-that the first number is at coordinate (0,0,0) the second at (1,0,0),
-the third at (2,0,0), etc. So, for example, say the image was 64 by
-64 by 20 in size, then the coordinates would go as (0,0,0) then
-(1,0,0) ... then (63,0,0) then (0,1,0) then (1,1,0) then (2,1,0)
-... then (63,1,0) then (0,2,0) ... then (63,63,0) then (0,0,1) then
-(1,0,1) ... until (63,63,19). Note that all coordinates start at 0,
-not 1, and that the first coordinate (i) here is the one that
-increases the fastest as you go through the list, followed by second
-(j) and then the third (k). These voxel coordinates - (i,j,k) - give
-spatial information (using information about how many voxels are in
-the three spatial directions) but do not attribute any anatomical
-information at all.
-
-<p>
-
-To go from voxel coordinates to more anatomically meaningful
-coordinates is the job of the <code>qform</code> and
-<code>sform</code> matrices that are stored in the NIfTI file. Note
-that these matrices only provide useful information if they have a
-non-zero <code>code</code>, since a zero <code>code</code> indicates
-that the matrix is "Unknown" and hence cannot be used. Having two
-matrices here is a common source of confusion. They were originally
-proposed so that two different coordinates could be kept track of -
-one representing the scanner coordinate system (the real space inside
-the scanner bore) and the other one relating to standard space
-coordinates (e.g. MNI152). However, in practice, it is rare that both
-contain different information as they are often set to be the same, or
-one of them is "Unknown" in which case the other contains all the
-useful information.
-
-<p>
-
-Either matrix (qform or sform) is used to convert the voxel coordinates into
-"real world" coordinates (also called continuous coordinates, or mm
-coordinates, or other names). These new coordinates - called (x,y,z)
-here - have units of mm, and can take any values, not just positive
-whole numbers like the (i,j,k) voxel coordinates. Note that FSLView
-displays both voxel and mm coordinates.
-[Aside: the conversion is done by
-multiplying the matrix with the voxel coordinate, reshaped as a 4x1
-vector with the last element equal to 1 - although this detail is not
-important for any of the discussion or understanding.]
-
-<p>
-
-If the <code>qform</code> (or <code>sform</code>) is set so that it
-gives information about scanner coordinates (as indicated by the
-<code>code</code>), then a standard convention is used to relate the
-coordinate values to the anatomy. The convention is: +x = Right; +y =
-Anterior; +z = Superior. That is, moving in the positive x-direction
-(so that the x-coordinate increases) will be moving to the right,
-etc. This now allows left and right to be distinguished, which is
-usually not possible just by looking at brain images. Hence this
-information is absolutely crucial and getting this right for the
-conversion of the image to NIfTI format is extremely important.
-If it is incorrect then it would be easy for left and right to be
-assigned incorrectly and all analysis results to be on the wrong side.
-The information from the <code>qform</code> and <code>sform</code>
-is what is used by FSLView to determine the labels that are shown on
-the image.
-
-<p>
-
-If the <code>sform</code> is set so that it gives information about
-standard space coordinates then the situation is the same as above,
-since the standard convention used above was chosen to be the same as
-the convention chosen for the standard space coordinate systems
-(MNI152 and Talairach). The main difference between the two
-situations is that the transformation to standard space (represented
-by the <code>sform</code> matrix) also involves scaling and shearing
-of the coordinate axes to make the brain "fit" the standard templates,
-whereas the transformation to scanner space coordinates is normally just a
-rotation and translation.
-
-<p>
-
-An aside on left-right conventions: it is possible to <i>store</i> an
-image in many different ways that are totally and completely
-equivalent in terms of the intensities and the (x,y,z) coordinates.
-What can be different is the voxel coordinates (and hence the order of
-the intensities stored in the file) but these are completely
-unimportant for all analysis purposes - they are purely related to the
-storage format, in this case NIfTI - only the (x,y,z) coordinates and
-the intensity values count with respect to the analysis. That being
-said, one common confusion arises when the left-right order of the
-storage is changed (but the mm coordinates and intensities are
-unchanged). For instance, imagine taking an image where the first
-voxel is on the left and then swapping the left-right order so that
-the new image is stored such that the first voxel is now the rightmost
-one, but modifying the <code>qform</code> and <code>sform</code>
-matrices appropriately so that this rightmost voxel still has the same
-(x,y,z) coordinate as it had before - just a different voxel
-coordinate. This kind of change will not affect any analysis in FSL
-or any programs that are fully NIfTI compliant. However, some
-programs are only happy with one sort of ordering (sometimes called
-left-handed/right-handed, or radiological/neurological, or RAS/LAS,
-etc.)
-This used to be the case for old versions of FSL, but is no longer true.
-But if only the order of the intensities in the file is swapped,
-<i>without</i> compensating for this in the <code>sform</code> and
-<code>qform</code> matrices, then the swapped version is no longer
-equivalent to the original. This is why both the data order and
-header information need to be kept in sync, and why running either
-<code>fslswapdim</code> or <code>fslorient</code> alone to change the
-orientation information is dangerous and usually incorrect.
-
-<p>
-
-An aside on display orientation: everything that has been said above
-about the NIfTI format refers to coordinates and data storage and has
-<i>nothing</i> to do with what way the images can be <i>displayed</i>
-in different viewing programs. Although the storage can be referred to
-as "radiological" or "neurological" this does not mean anything with
-respect to the displayed orientation. A valid NIfTI image can be
-displayed in any orientation that the viewing tool chooses, with the
-left side of the brain shown on the right side of the screen (so
-called radiological convention) or the other way around (neurological
-convention). It is also possible to display the inferior side of the
-brain at the top of the image, or any other configuration. It is
-entirely up to the display software how it chooses to show the image
-on the screen. What the NIfTI format does do is provide information
-to determine how to label the different parts of the image (with mm
-coordinates or anatomical labels such as left, right, anterior,
-posterior, superior and inferior). As long as the display tool
-correctly interprets this information and keeps it consistent with its
-choice of display orientation, there is no conflict between any type
-of NIfTI image and any displayed orientation.
-
-<p><HR><FONT SIZE=1>Copyright © 2000-2008, University of
-Oxford. Written by <A
-HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A> and M. Jenkinson.</FONT>
-
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-
-</BODY></HTML>
-
diff --git a/fsl2ascii.cc b/fsl2ascii.cc
index 92ded9c..c790df2 100755
--- a/fsl2ascii.cc
+++ b/fsl2ascii.cc
@@ -25,14 +25,14 @@ int fmrib_main(int argc, char *argv[])
string output_name=string(argv[2]);
ofstream output_file;
int i,j,k,t;
- for(t=0;t<input_volume.tsize();t++)
+ for(t=0;t<=input_volume.maxt();t++)
{
output_file.open((output_name+num2str(t,5)).c_str(),ofstream::out);
- for(k=0;k<input_volume.zsize();k++)
+ for(k=0;k<=input_volume.maxz();k++)
{
- for(j=0;j<input_volume.ysize();j++)
+ for(j=0;j<=input_volume.maxy();j++)
{
- for(i=0;i<input_volume.xsize();i++)
+ for(i=0;i<=input_volume.maxx();i++)
{
output_file << input_volume(i,j,k,t) << " ";
}
diff --git a/fslcc.cc b/fslcc.cc
index e82a094..5de2041 100755
--- a/fslcc.cc
+++ b/fslcc.cc
@@ -1,6 +1,6 @@
// fslcc.cc cross-correlate two time series timepoint by timepoint
// Steve Smith and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2001-2015 University of Oxford
+// Copyright (C) 2001-2013 University of Oxford
// CCOPYRIGHT
#include "newimage/newimageall.h"
@@ -36,7 +36,7 @@ int fmrib_main(int argc, char *argv[])
read_volume4D(input_volume1,input_name1);
read_volume4D(input_volume2,input_name2);
- if (!samesize(input_volume1,input_volume2,3))
+ if (input_volume1.maxx() != input_volume2.maxx() || input_volume1.maxy() != input_volume2.maxy() || input_volume1.maxz() != input_volume2.maxz())
{
cerr << "Error: Mismatch in image dimensions" << endl;
return 1;
@@ -45,7 +45,7 @@ int fmrib_main(int argc, char *argv[])
volume<T> mask;
if(fnmask.value().length()>0){
read_volume(mask,fnmask.value());
- if(!samesize(input_volume1,mask,3)){
+ if(!samesize(input_volume1[0],mask)){
cerr << "Error: Mismatch in mask dimensions" << endl;
return 1;
}
@@ -53,6 +53,7 @@ int fmrib_main(int argc, char *argv[])
mask=input_volume1[0];
mask=1;
}
+
if ( !nodemean.value() ) {
for(int t1=0;t1<=input_volume1.maxt();t1++)
diff --git a/fslcheck.cc b/fslcheck.cc
deleted file mode 100644
index 899f012..0000000
--- a/fslcheck.cc
+++ /dev/null
@@ -1,140 +0,0 @@
-/* fslcheck.cc - Utility to check validity of avw header file
-
- Peter Bannister and Matthew Webster, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2007 University of Oxford */
-
-/* CCOPYRIGHT */
-
-
-#include <cmath>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <cstdlib>
-#include <cstdio>
-#include <string>
-#include <sstream>
-
-#include "newmatap.h"
-#include "newmatio.h"
-#include "newimage/newimageall.h"
-#include "utils/options.h"
-#include "newimage/fmribmain.h"
-
-using namespace MISCMATHS;
-using namespace NEWMAT;
-using namespace NEWIMAGE;
-using namespace Utilities;
-
-string title="fslcheck (Version 1.0)\nChecks Header file info for voxel dimensions\nCopyright(c) 2001, University of Oxford (Peter R Bannister)";
-string examples="fslcheck -i <header_file>\n";
-
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, no_argument);
-Option<bool> verbose(string("-v,--verbose"), false,
- string("switch on diagnostic messages"),
- false, no_argument);
-Option<string> inputname(string("-i,--in"), string(""),
- string("filename of input timeseries"),
- true, requires_argument);
-const float tolerance = 0.00000001;
-
-template <class T>
-int fmrib_main(int argc, char* argv[])
-{
- volume4D<T> timeseries;
- volumeinfo vinfo;
- float x_dim, y_dim, z_dim, t_dim;
- short datatype;
-
- if (inputname.set()) {
- if (verbose. value()) { cout << "Reading header file" << endl; }
- read_volume4D_hdr_only(timeseries,inputname. value(),vinfo);
- }
-
- if (fabs(timeseries. xdim()) <= tolerance) {
- do {
- cerr << "Invalid voxel x-dimension (" << timeseries. xdim() << " mm): Please enter a new value" << endl;
- cin >> x_dim;
- } while (fabs(x_dim) <= tolerance);
- timeseries. setxdim(x_dim);
- }
-
- if (fabs(timeseries. ydim()) <= tolerance) {
- do {
- cerr << "Invalid voxel y-dimension (" << timeseries. ydim() << " mm): Please enter a new value" << endl;
- cin >> y_dim;
- } while (fabs(y_dim) <= tolerance);
- timeseries. setydim(y_dim);
- }
-
- if (fabs(timeseries. zdim()) <= tolerance) {
- do {
- cerr << "Invalid voxel z-dimension (" << timeseries. zdim() << " mm): Please enter a new value" << endl;
- cin >> z_dim;
- } while (fabs(z_dim) <= tolerance);
- timeseries. setzdim(z_dim);
- }
-
- if (fabs(timeseries. tdim()) <= tolerance) {
- do {
- cerr << "Invalid TR (" << timeseries. tdim() << " secs): Please enter a new value" << endl;
- cin >> t_dim;
- } while (fabs(t_dim) <= tolerance);
- timeseries. settdim(t_dim);
- }
-
- // set bitpix correctly (via FslSetDataType) - NB: type T = datatype
- FslGetDataType(&vinfo,&datatype);
- FslSetDataType(&vinfo,datatype);
- // read in whole file(!) and save it again
- volume4D<T> tmp;
- read_volume4D(tmp, inputname.value());
- save_volume4D_filetype(tmp, inputname.value(), FslGetFileType(&vinfo), vinfo);
- return 0;
-}
-
-int main (int argc,char** argv)
-{
- Tracer tr("main");
-
- OptionParser options(title, examples);
-
- try {
- options.add(inputname);
- options.add(help);
- options.add(verbose);
-
- options.parse_command_line(argc, argv);
-
- if ( (help.value()) || (!options.check_compulsory_arguments(true)) )
- {
- options.usage();
- exit(EXIT_FAILURE);
- }
-
- if ( inputname.unset())
- {
- options.usage();
- cerr << endl
- << "--in or -i MUST be used."
- << endl;
- exit(EXIT_FAILURE);
- }
-
- } catch(X_OptionError& e) {
- options.usage();
- cerr << endl << e.what() << endl;
- exit(EXIT_FAILURE);
- } catch(std::exception &e) {
- cerr << e.what() << endl;
- }
-
- int retval=call_fmrib_main(dtype(inputname.value()), argc, argv);
- if (retval!=0) {
- cerr << "Failed to correctly read file, please check the .hdr using fslhd" << endl;
- } else return retval;
-}
-
diff --git a/fslcorrecthd.cc b/fslcorrecthd.cc
deleted file mode 100755
index 261bf5f..0000000
--- a/fslcorrecthd.cc
+++ /dev/null
@@ -1,94 +0,0 @@
-// fslcorrecthd.cc - check and correct a nifti file for bad vox-offset
-// Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2007 University of Oxford
-// CCOPYRIGHT
-
-#include "newimage/newimageall.h"
-#include "fslio/fslio.h"
-#include <iostream>
-using namespace NEWIMAGE;
-
-void print_usage(const string& progname)
-{
- cout << endl;
- cout << "Usage: fslcorrecthd <input> <output>" << endl;
- cout << " Note that fslcorrecthd only operates on uncompressed NIFTI or ANALYZE files" << endl;
-}
-
-int main(int argc,char *argv[])
-{
- if (argc < 3)
- {
- print_usage(string(argv[0]));
- return 1;
- }
- FSLIO* fslio=NULL;
- fslio = FslOpen(FslMakeBaseName(argv[1]),"rb");
- FslClose(fslio);
- struct dsr *hdr;
- hdr = (struct dsr *)calloc(1,sizeof(struct dsr));
- FslReadRawHeader(hdr,fslio->niftiptr->fname);
- if (fslio->niftiptr->byteorder != nifti_short_order())
- {
- cout << "Byte swapping" << endl;
- AvwSwapHeader(hdr);
- }
- //check nifti-libs output versus raw header info
- int offset =(int) ( fslio->niftiptr->iname_offset - hdr->dime.vox_offset );
- int minft=(int)MIN(fslio->niftiptr->iname_offset,hdr->dime.vox_offset);
- cout << "number of bytes wrong: " << offset << endl << "start at byte location: " << minft << endl;
-
- if (offset==0) {
- cout << "No byte correction needed, exiting." << endl;
- return 0;
- }
-
- if (FslIsCompressedFileType(FslGetFileType(fslio))) {
- cerr << "Error: fslcorrecthd requires uncompressed input" << endl;
- return 1;
- }
-
- ifstream input_file;
- ofstream output_file;
- char *temp,*outputName,*inputName;
- FslGetHdrImgNames(argv[2],fslio,&temp,&outputName);
- FslGetHdrImgNames(argv[1],fslio,&temp,&inputName);
- char byte[1];
- input_file.open(inputName,ios::in | ios :: binary);
- output_file.open(outputName,ofstream::out | ofstream::binary);
-
- for(int i=1;i<=minft;i++) //Write Header
- {
- input_file.read(byte,1);
- if (input_file.eof()) break;
- output_file.write(byte,1);
- }
-
- for(int i=1;i<=abs(offset) && offset>0;i++) //Pad if we have missing 4 bytes
- {
- byte[0]=0;
- output_file.write(byte,1);
- }
-
- for(int i=1;i<=abs(offset) && offset<0;i++) //Read past bad extensions/junk
- {
- input_file.read(byte,1);
- }
-
- while(true) //Copy the data
- {
- input_file.read(byte,1);
- if (input_file.eof()) break;
- output_file.write(byte,1);
- }
- output_file.close();
- input_file.close();
-
- system(("FSLOUTPUTTYPE=NIFTI; ${FSLDIR}/bin/fslmaths " + string(outputName)).c_str()); //To clean up header
- free(temp);
- free(outputName);
- free(hdr);
- return 0;
-}
-
-
diff --git a/fsldecorr4d.cc b/fsldecorr4d.cc
deleted file mode 100644
index 9401239..0000000
--- a/fsldecorr4d.cc
+++ /dev/null
@@ -1,325 +0,0 @@
-/* fsldecorr4d.cc
-
- Mark Jenkinson, FMRIB Image Analysis Group
-
- Copyright (C) 2007 University of Oxford */
-
-/* CCOPYRIGHT */
-
-
-// Decorrelates a set of separable 4D components from
-// a 4D dataset
-
-#include "newimage/newimageall.h"
-#include "miscmaths/miscmaths.h"
-#include "utils/options.h"
-
-using namespace NEWIMAGE;
-using namespace MISCMATHS;
-
-using namespace Utilities;
-
-// The two strings below specify the title and example usage that is
-// printed out as the help or usage message
-
-string title="fsldecorr4d (Version 1.0)\nCopyright(c) 2004, University of Oxford (Mark Jenkinson)\nRemoves 4D components (by decorrelation) from a 4D dataset.\nEach component needs to be specified by a separate timecourse and spatial map.\nThe spatial maps are input as a single 4D file and the timecourses as a text matrix (with each column being a timecourse with the same ordering as the corresponding spatial maps.\n";
-string examples="fsldecorr4d -s <spatial maps> -t <timecourses> -i <input> -o <output> [-m mask]";
-
-// Each (global) object below specificies as option and can be accessed
-// anywhere in this file (since they are global). The order of the
-// arguments needed is: name(s) of option, default value, help message,
-// whether it is compulsory, whether it requires arguments
-// Note that they must also be included in the main() function or they
-// will not be active.
-
-Option<bool> verbose(string("-v,--verbose"), false,
- string("switch on diagnostic messages"),
- false, no_argument);
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, no_argument);
-Option<string> smapname(string("-s"), string(""),
- string("~<filename>\tinput set of spatial maps (4D)"),
- false, requires_argument);
-Option<string> tcname(string("-t"), string(""),
- string("~<filename>\tinput set of timecourses (text matrix)"),
- false, requires_argument);
-Option<string> maskname(string("-m"), string(""),
- string("~<filename>\tinput 3D mask"),
- false, requires_argument);
-Option<string> outname(string("-o"), string(""),
- string("~<filename>\toutput 4D dataset"),
- true, requires_argument);
-Option<string> inname(string("-i"), string(""),
- string("~<filename>\tinput 4D dataset"),
- true, requires_argument);
-
-int nonoptarg;
-
-
-int decorr1D(volume4D<float>& vol, const Matrix& tc, const volume<float>& mask)
-{
- int nt=tc.Nrows();
- int nc=tc.Ncols();
- Matrix XX(nc,nc);
- ColumnVector Y(nt), Beta(nc);
- XX = tc.t() * tc;
- if (verbose.value()) { cout << "Processing slices "; }
- for (int z=vol[0].minz(); z<=vol[0].maxz(); z++) {
- for (int y=vol[0].miny(); y<=vol[0].maxy(); y++) {
- for (int x=vol[0].minx(); x<=vol[0].maxx(); x++) {
- if (mask(x,y,z)>0.5) {
- for (int t=0; t<nt; t++) { Y(t+1) = vol(x,y,z,t); }
- Beta = pinv(XX) * tc.t() * Y;
- Y -= tc * Beta;
- for (int t=0; t<nt; t++) { vol(x,y,z,t) = Y(t+1); }
- }
- }
- }
- if (verbose.value()) { cout << "."; }
- }
- if (verbose.value()) { cout << endl; }
- return 0;
-}
-
-int decorr4D(volume4D<float>& vol, const Matrix& tc,
- const volume4D<float>& smaps, const volume<float>& mask)
-{
- int nt=tc.Nrows();
- int nc=tc.Ncols();
-
- // set up required matrices
- Matrix XX(nc,nc);
- ColumnVector XY(nc);
- XY=0.0; XX=0.0;
-
- if (verbose.value()) { cout << "Calculating matrix values:" << endl; }
- // calculate matrix elements (4D correlations)
- for (int n=1; n<=nc; n++) {
- if (verbose.value()) { cout << "Component #" << n << endl; }
- for (int t=0; t<nt; t++) {
- for (int z=smaps[n-1].minz(); z<=smaps[n-1].maxz(); z++) {
- for (int y=smaps[n-1].miny(); y<=smaps[n-1].maxy(); y++) {
- for (int x=smaps[n-1].minx(); x<=smaps[n-1].maxx(); x++) {
- XY(n) += smaps(x,y,z,n-1) * tc(t+1,n) * vol(x,y,z,t);
- }
- }
- }
- }
- for (int m=1; m<=n; m++) {
- volume<float> tmp;
- tmp = smaps[n-1] * smaps[m-1];
- XX(m,n) = tmp.sum();
- double tval=0.0;
- for (int t=0; t<nt; t++) {
- tval += tc(t+1,n) * tc(t+1,m);
- }
- XX(m,n) *= tval;
- XX(n,m) = XX(m,n);
- }
- }
- if (verbose.value()) { cout << "XY = " << XY.t()/nt << endl; }
- if (verbose.value()) { cout << "XX = " << (XX/nt)/nt << endl; }
-
-
- if (verbose.value()) { cout << "Finding amplitudes" << endl; }
- // find amplitudes for each component
- ColumnVector Beta(nc);
- Beta = pinv(XX)*XY;
- if (verbose.value()) { cout << "Amplitudes = " << Beta.t() << endl << endl; }
-
-
- if (verbose.value()) { cout << "Removing components" << endl; }
- // remove components from input data
- for (int n=1; n<=nc; n++) {
- for (int t=0; t<nt; t++) {
- for (int z=smaps[n-1].minz(); z<=smaps[n-1].maxz(); z++) {
- for (int y=smaps[n-1].miny(); y<=smaps[n-1].maxy(); y++) {
- for (int x=smaps[n-1].minx(); x<=smaps[n-1].maxx(); x++) {
- vol(x,y,z,t) -= Beta(n) * smaps(x,y,z,n-1) * tc(t+1,n);
- }
- }
- }
- }
- }
-
- return 0;
-}
-
-
-int decorr3D(volume4D<float>& vol, const volume4D<float>& smaps,
- const volume<float>& mask)
-{
- int nt=vol.tsize();
- int nc=smaps.tsize();
-
- // set up required matrices
- Matrix XX(nc,nc);
- ColumnVector XY(nc);
- XY=0.0; XX=0.0;
-
- // calculate matrix elements (4D correlations)
- for (int n=1; n<=nc; n++) {
- for (int m=1; m<=n; m++) {
- volume<float> tmp;
- tmp = smaps[n-1] * smaps[m-1];
- XX(m,n) = tmp.sum();
- XX(n,m) = XX(m,n);
- }
- }
- if (verbose.value()) { cout << "XX = " << (XX/nt)/nt << endl; }
- Matrix pinvXX;
- pinvXX=pinv(XX);
-
- if (verbose.value()) { cout << "Calculating matrix values:" << endl; }
- // calculate matrix elements (4D correlations)
- for (int t=0; t<nt; t++) {
- if (verbose.value()) { cout << "."; }
- XY=0.0;
- for (int n=1; n<=nc; n++) {
- for (int z=smaps[n-1].minz(); z<=smaps[n-1].maxz(); z++) {
- for (int y=smaps[n-1].miny(); y<=smaps[n-1].maxy(); y++) {
- for (int x=smaps[n-1].minx(); x<=smaps[n-1].maxx(); x++) {
- XY(n) += smaps(x,y,z,n-1) * vol(x,y,z,t);
- }
- }
- }
- }
- // find amplitudes for each component
- ColumnVector Beta(nc);
- Beta = pinvXX*XY;
- // remove components from input data
- for (int n=1; n<=nc; n++) {
- for (int z=smaps[n-1].minz(); z<=smaps[n-1].maxz(); z++) {
- for (int y=smaps[n-1].miny(); y<=smaps[n-1].maxy(); y++) {
- for (int x=smaps[n-1].minx(); x<=smaps[n-1].maxx(); x++) {
- vol(x,y,z,t) -= Beta(n) * smaps(x,y,z,n-1);
- }
- }
- }
- }
- }
- if (verbose.value()) { cout << endl; }
-
- return 0;
-}
-
-
-
-int do_work(int argc, char *argv[])
-{
- volume4D<float> vin;
- read_volume4D(vin,inname.value());
-
- // ** MASK ** //
-
- volume<float> mask;
- if (maskname.set()) {
- read_volume(mask,maskname.value());
- } else {
- mask = vin[0];
- mask = 1.0;
- }
-
- if (!samesize(vin[0],mask)) {
- cerr << "ERROR: Mask and Input volumes have different (x,y,z) size."
- << endl;
- return 2;
- }
-
- mask.binarise(1e-8); // arbitrary "0" threshold
-
-
- // ** TIME COURSES ** //
-
- Matrix tc;
- if (tcname.set()) {
- tc = read_ascii_matrix(tcname.value());
- if (tc.Nrows() != vin.tsize()) {
- cerr << "ERROR: Different number of timepoints in timecourse file and input volume." << endl;
- return 3;
- }
- // demean timecourses (to stop any correlation with the mean)
- tc = remmean(tc);
- }
-
- // ** SPATIAL MAPS ** //
-
- // if no smaps specified then go for simple 1D decorrelation
- volume4D<float> smaps;
- if (smapname.set()) {
- // if smaps are specified then do the full 4D decorrelation
- read_volume4D(smaps,smapname.value());
- if (!samesize(vin[0],smaps[0])) {
- cerr << "ERROR: Spatial maps and Input volumes have different (x,y,z) size."
- << endl;
- return 1;
- }
- if (tcname.set() && (tc.Ncols() != smaps.tsize())) {
- cerr << "ERROR: Different number of components for timecourses and spatial maps." << endl;
- return 4;
- }
-
- // mask spatial maps
- smaps *= mask;
- // demean spatial maps (wrt mask)
- for (int n=0; n<smaps.tsize(); n++) {
- smaps[n] -= ((float) smaps[n].mean())*mask;
- }
- }
-
-
- // ** DECORRELATION ** //
-
- int retval=0;
- if (smapname.set() && tcname.set()) {
- retval = decorr4D(vin,tc,smaps,mask);
- }
- if (!smapname.set() && tcname.set()) {
- retval = decorr1D(vin,tc,mask);
- }
- if (smapname.set() && !tcname.set()) {
- retval = decorr3D(vin,smaps,mask);
- }
- if (!smapname.set() && !tcname.set()) {
- cerr << "ERROR: Must pass in either spatial maps or timecourses or both"
- << endl;
- return 3;
- }
-
- // save the result
- if (retval==0) save_volume4D(vin,outname.value());
-
- return retval;
-}
-
-
-int main(int argc,char *argv[])
-{
-
- Tracer tr("main");
- OptionParser options(title, examples);
-
- options.add(inname);
- options.add(outname);
- options.add(smapname);
- options.add(tcname);
- options.add(maskname);
- options.add(verbose);
- options.add(help);
-
- nonoptarg = options.parse_command_line(argc, argv);
-
- // line below stops the program if the help was requested or
- // a compulsory option was not set
- if ( (help.value()) || (!options.check_compulsory_arguments(true)) )
- {
- options.usage();
- exit(EXIT_FAILURE);
- }
-
-
- // OK, now do the job ...
- return do_work(argc,argv);
-}
-
diff --git a/fslfromascii.cc b/fslfromascii.cc
deleted file mode 100755
index 7ff89f4..0000000
--- a/fslfromascii.cc
+++ /dev/null
@@ -1,37 +0,0 @@
-// fsl2ascii.cc - convert AVW to raw ASCII text
-// Stephen Smith and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2001-2005 University of Oxford
-// COPYRIGHT
-#include "newimage/newimageall.h"
-#include "miscmaths/miscmaths.h"
-#include <fstream>
-
-using namespace NEWIMAGE;
-using namespace MISCMATHS;
-
-void print_usage(const string& progname) {
- cout << endl;
- cout << "Usage: fslfromascii <input> <xsize> <ysize> <zsize> <tsize> <output>" << endl;
-}
-
-
-int main(int argc,char *argv[])
-{
- if (argc != 7)
- {
- print_usage(string(argv[0]));
- return 1;
- }
- volume4D<float> output_volume(atoi(argv[2]),atoi(argv[3]),atoi(argv[4]),atoi(argv[5]));
- ifstream input(argv[1]);
- for(int t=0;t<=output_volume.maxt();t++)
- for(int z=0;z<=output_volume.maxz();z++)
- for(int y=0;y<=output_volume.maxy();y++)
- for(int x=0;x<=output_volume.maxx();x++)
- input >> output_volume(x,y,z,t);
- save_volume4D(output_volume,string(argv[6]));
- input.close();
- return 0;
-}
-
-
diff --git a/tests/avw2ascii_test.sh b/tests/avw2ascii_test.sh
deleted file mode 100755
index d3527e3..0000000
--- a/tests/avw2ascii_test.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-#test 3D volume
-avw2ascii $FSLTESTDIR/common/filtered_func_data.nii.gz test
-../avw2ascii++ $FSLTESTDIR/common/filtered_func_data.nii.gz test2
-flag=0
-i=0
-while [ $i -lt 100 ]
-do
-if [ $i -lt 10 ]
-then
-cmp test0000${i} test20000${i}
-else
-cmp test000${i} test2000${i}
-fi
-j=$?
-echo $i $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-i=`expr $i + 1`
-done
-
-rm test*
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avw2ascii++"
-else
-echo "All comparisons zero. No problems detected with avw2ascii++"
-fi
\ No newline at end of file
diff --git a/tests/avwcc_test.sh b/tests/avwcc_test.sh
deleted file mode 100755
index 10d64c1..0000000
--- a/tests/avwcc_test.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-#test 3D volume
-echo "Running awcc non-compliant voxel dimension test"
-avwcc $FSLTESTDIR/common/avg152T1_brain.img $FSLTESTDIR/common/filtered_func_data.nii.gz > test
-../avwcc++ $FSLTESTDIR/common/avg152T1_brain.img $FSLTESTDIR/common/filtered_func_data.nii.gz > test2
-flag=0
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-avwcc $FSLTESTDIR/common/filtered_func_data.nii.gz $FSLTESTDIR/common/filtered_func_data.nii.gz > test
-../avwcc++ $FSLTESTDIR/common/filtered_func_data.nii.gz $FSLTESTDIR/common/filtered_func_data.nii.gz > test2
-flag=0
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwcc"
-else
-echo "All comparisons zero. No problems detected with avwcc"
-fi
\ No newline at end of file
diff --git a/tests/avwcpgeom_test.sh b/tests/avwcpgeom_test.sh
deleted file mode 100755
index d128a9f..0000000
--- a/tests/avwcpgeom_test.sh
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/bin/sh
-flag=0
-cp $FSLTESTDIR/common/filtered_func_data.nii.gz temp.nii.gz
-cp $FSLTESTDIR/common/filtered_func_data.nii.gz temp2.nii.gz
-avwcpgeom $FSLTESTDIR/common/avg152T1_brain.hdr temp.nii.gz
-../avwcpgeom++ $FSLTESTDIR/common/avg152T1_brain.hdr temp2.nii.gz
-
-cmp temp.nii.gz temp2.nii.gz
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 4D:3D comparison in avwcpgeom++"
-flag=1
-fi
-
-rm temp*
-
-cp $FSLTESTDIR/common/filtered_func_data.nii.gz temp.nii.gz
-cp $FSLTESTDIR/common/filtered_func_data.nii.gz temp2.nii.gz
-avwcpgeom $FSLTESTDIR/common/avg152T1_brain.hdr temp.nii.gz -d
-../avwcpgeom++ $FSLTESTDIR/common/avg152T1_brain.hdr temp2.nii.gz -d
-
-cmp temp.nii.gz temp2.nii.gz
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 4D:3D comparison in avwcpgeom++"
-flag=1
-fi
-
-rm temp*
-
-cp $FSLTESTDIR/common/avg152T1_brain.hdr temp.hdr
-cp $FSLTESTDIR/common/avg152T1_brain.img temp.img
-cp $FSLTESTDIR/common/avg152T1_brain.hdr temp2.hdr
-cp $FSLTESTDIR/common/avg152T1_brain.img temp2.img
-
-avwcpgeom $FSLTESTDIR/common/filtered_func_data.nii.gz temp
-../avwcpgeom++ $FSLTESTDIR/common/filtered_func_data.nii.gz temp2
-
-cmp temp.hdr temp2.hdr
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 3D:4D comparison in avwcpgeom++"
-flag=1
-fi
-
-cmp temp.img temp2.img
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 3D:4D comparison in avwcpgeom++"
-flag=1
-fi
-
-rm temp*
-
-cp $FSLTESTDIR/common/avg152T1_brain.hdr temp.hdr
-cp $FSLTESTDIR/common/avg152T1_brain.img temp.img
-cp $FSLTESTDIR/common/avg152T1_brain.hdr temp2.hdr
-cp $FSLTESTDIR/common/avg152T1_brain.img temp2.img
-
-avwcpgeom $FSLTESTDIR/common/filtered_func_data.nii.gz temp -d
-../avwcpgeom++ $FSLTESTDIR/common/filtered_func_data.nii.gz temp2 -d
-
-cmp temp.hdr temp2.hdr
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 3D:4D comparison in avwcpgeom++"
-flag=1
-fi
-
-cmp temp.img temp2.img
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in 3D:4D comparison in avwcpgeom++"
-flag=1
-fi
-
-rm temp*
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwcpgeom++"
-else
-echo "All comparisons zero. No problems detected with avwcpgeom++"
-fi
\ No newline at end of file
diff --git a/tests/avwcreatehd_test.sh b/tests/avwcreatehd_test.sh
deleted file mode 100755
index 192b49d..0000000
--- a/tests/avwcreatehd_test.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/sh
-flag=0
-avwcreatehd header.xml temp
-../avwcreatehd++ header.xml temp2
-cmp temp.nii.gz temp2.nii.gz
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in xml header create in avwcreatehd++"
-flag=1
-fi
-
-rm temp*
-
-avwcreatehd 10 10 10 10 2 2 2 1 0 0 0 4 temp
-../avwcreatehd++ 10 10 10 10 2 2 2 1 0 0 0 4 temp2
-cmp temp.nii.gz temp2.nii.gz
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in manual header create in avecreatehd++"
-flag=1
-fi
-
-rm temp*
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwcreatehd++"
-else
-echo "All comparisons zero. No problems detected with avwcreatehd++"
-fi
\ No newline at end of file
diff --git a/tests/avwhd_test.sh b/tests/avwhd_test.sh
deleted file mode 100755
index 7209514..0000000
--- a/tests/avwhd_test.sh
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-avwhd $FSLTESTDIR/common/avg152T1_brain.hdr > test
-../avwhd++ $FSLTESTDIR/common/avg152T1_brain.hdr > test2
-flag=0
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-avwhd $FSLTESTDIR/common/filtered_func_data.nii.gz > test
-../avwhd++ $FSLTESTDIR/common/filtered_func_data.nii.gz > test2
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-avwhd -x $FSLTESTDIR/common/avg152T1_brain.hdr > test
-../avwhd++ -x $FSLTESTDIR/common/avg152T1_brain.hdr > test2
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-avwhd -x $FSLTESTDIR/common/filtered_func_data.nii.gz > test
-../avwhd++ -x $FSLTESTDIR/common/filtered_func_data.nii.gz > test2
-cmp test test2
-j=$?
-echo $j
-if [ $j -ne 0 ]
-then
-echo "Problem found in this comparision"
-flag=1
-fi
-
-rm test*
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwhd++"
-else
-echo "All comparisons zero. No problems detected with avwhd++"
-fi
\ No newline at end of file
diff --git a/tests/avwinterleave_test.sh b/tests/avwinterleave_test.sh
deleted file mode 100755
index a150e7d..0000000
--- a/tests/avwinterleave_test.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/bin/sh
-flag_maths=0
-flag_bit=0
-avwinterleave $FSLTESTDIR/common/vol0000.nii.gz $FSLTESTDIR/common/vol0001.nii.gz temp1
-../avwinterleave++ $FSLTESTDIR/common/vol0000.nii.gz $FSLTESTDIR/common/vol0001.nii.gz temp2
-cmp temp1.nii.gz temp2.nii.gz
-output2=$?
-if [ $output2 -ne 0 ]
-then
-flag_bit=1
-echo "Standard merge failed bit-comparison test in avwinterleave++"
-fi
-avwmaths temp1 -sub temp2 temp3
-output1=`avwstats temp3 -m`
-echo "Result of interleave test:" $output1 $output2
-if [ $output1 != 0.000000 ];
-then
-flag_maths=1
-echo "standard merge failed maths test in avwinterleave++";
-fi
-
-rm temp*
-
-avwinterleave $FSLTESTDIR/common/vol0000.nii.gz $FSLTESTDIR/common/vol0001.nii.gz temp1 -i
-../avwinterleave++ $FSLTESTDIR/common/vol0000.nii.gz $FSLTESTDIR/common/vol0001.nii.gz temp2 -i
-cmp temp1.nii.gz temp2.nii.gz
-output2=$?
-if [ $output2 -ne 0 ]
-then
-flag_bit=1
-echo "inverse merge failed bit-comparison test in avwinterleave++"
-fi
-avwmaths temp1 -sub temp2 temp3
-output1=`avwstats temp3 -m`
-echo "Result of inverse interleave test:" $output1 $output2
-if [ $output1 != 0.000000 ];
-then
-flag_maths=1
-echo "inverse merge failed maths test in avwinterleave++";
-fi
-
-rm temp*
-
-echo ""
-if [ $flag_maths -ne 0 -o $flag_bit -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwinterleave++"
-else
-echo "All comparisons zero. No problems detected with avwinterleave++"
-fi
\ No newline at end of file
diff --git a/tests/avwmaths_test.sh b/tests/avwmaths_test.sh
deleted file mode 100755
index dbe012c..0000000
--- a/tests/avwmaths_test.sh
+++ /dev/null
@@ -1,389 +0,0 @@
-#!/bin/sh
-#testing avwmaths
-flag=0
-#avwmaths volume test
-for setting in -T -X -Y -Z
-do
-for loop in mean std max maxn median
-do
-set2=`echo $setting$loop`
-../avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz $set2 temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $set2 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $setting$loop test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $setting$loop test in avwmaths++";
-fi
-rm temp*
-done
-set2=`echo ${setting}perc`
-avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz $set2 40 temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $set2 40 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $set2 test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $set2 test in avwmaths++";
-fi
-rm temp*
-set2=`echo ${setting}ar1`
-set3=`echo ${setting}mean`
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $set3 tempmean -odt float
-if [ $set2 = -Xar1 ]
-then
-avwmerge -x tempmean tempmean tempmean #2
-avwmerge -x tempmean tempmean tempmean #4
-avwmerge -x tempmean tempmean tempmean #8
-avwmerge -x tempmean tempmean tempmean #16
-avwmerge -x tempmean tempmean tempmean tempmean tempmean #32
-fi
-if [ $set2 = -Yar1 ]
-then
-avwmerge -y tempmean tempmean tempmean #2
-avwmerge -y tempmean tempmean tempmean #4
-avwmerge -y tempmean tempmean tempmean #8
-avwmerge -y tempmean tempmean tempmean #16
-avwmerge -y tempmean tempmean tempmean tempmean tempmean #32
-fi
-if [ $set2 = -Zar1 ]
-then
-../avwmerge -z tempout tempmean tempmean tempmean #3
-../avwmerge -z tempmean tempout tempout tempout tempout tempout tempout tempout #21
-fi
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -sub tempmean tempmean -odt float
-../avwmaths_32R tempmean $set2 temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $set2 temp1 -odt float
-
-../avwmaths++ temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $set2 test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $set2 test in avwmaths++";
-fi
-rm temp*
-
-done
-
-
-
-
-
-
-
-
-
-
-
-
-
-ip_32R $FSLTESTDIR/common/filtered_func_data.nii.gz temp 0 -t 10 60
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -bptf 10 60 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of bptf test:" $output1
-limit=0.05 #Good value, test seems sensitive to changes in algorithm/input errors
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with bptf test in avwmaths++";
-else echo "bptf test within tolerance";
-fi
-rm temp*
-
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean tempvol
-../avwconv --dilate -b 10 -i tempvol -o temp
-../avwmaths++ tempvol -kernel box 10 -dilF temp1
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of avwconv erosion test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with avwconv erosion test in avwmaths++";
-else echo "avwconv erosion test within tolerance";
-fi
-rm temp*
-
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean tempvol
-../avwconv --erode -b 10 -i tempvol -o temp
-../avwmaths++ tempvol -kernel box 10 -eroF temp1
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of avwconv dilation edge test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with avwconv dilation test in avwmaths++";
-else echo "avwconv dilation test within tolerance";
-fi
-rm temp*
-
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean tempvol
-avwconv -b 40 -i tempvol -o temp
-../avwmaths++ tempvol -kernel box 40 -fmeanu temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of large box convolve edge test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with large box convolve test in avwmaths++";
-else echo "large box convolve test within tolerance";
-fi
-rm temp*
-
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean tempvol
-../avwconv -b 8 -i tempvol -o temp
-../avwmaths++ tempvol -kernel box 8 -fmeanu temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of small box convolve edge test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with small box convolve test in avwmaths++";
-else echo "small box convolve test within tolerance";
-fi
-rm temp*
-
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean tempvol
-../avwconv -s 12 --median -i tempvol -o temp
-../avwmaths++ tempvol -kernel sphere 12 -fmedian temp1
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of spherical kernel test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with spherical kernel test in avwmaths++";
-else echo "spherical kernel test within tolerance";
-fi
-rm temp*
-
-ip_16SI $FSLTESTDIR/common/filtered_func_data.nii.gz temp 0 -S 3
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -kernel box 12 -fmedian temp1
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of ip median box kernel test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with ip median box kernel test in avwmaths++";
-fi
-rm temp*
-
-ip_32R $FSLTESTDIR/common/filtered_func_data.nii.gz temp 0 -s 4
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -kernel gauss 4 -fmean temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of ip gaussian kernel test:" $output1
-limit=0.0001
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with ip gaussian kernel test in avwmaths++";
-else echo "ip gaussian kernel test within tolerance";
-fi
-rm temp*
-
-avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz -roi 10 30 10 30 10 30 0 10 temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -roi 10 30 10 30 10 30 0 10 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of roi test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with roi test in avwmaths++";
-fi
-rm temp*
-
-ip_32R $FSLTESTDIR/common/filtered_func_data.nii.gz temp 90 -m mask1
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -thrp 90 -Tmin -bin mask -odt float
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -mas mask temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of ip thresholding test:" $output1
-limit=1
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with ip thresholding (-thrmt) test in avwmaths++";
-else echo "ip thresholding test within tolerance";
-fi
-rm temp*
-rm mask*
-
-
-for loop in -sub -add -mul -div -mas -max -min
-do
-avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz $loop $FSLTESTDIR/common/mask.nii.gz temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $loop $FSLTESTDIR/common/mask.nii.gz temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $loop volume test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $loop volume test in avwmaths++";
-fi
-rm temp*
-done
-
-
-for loop in -exp -log -sqr -sqrt -abs -edge -bin
-do
-avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz $loop temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $loop temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $loop volume test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $loop volume test in avwmaths++";
-fi
-rm temp*
-done
-
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -exp infvol -odt float
-for loop in -nan -nanm
-do
-avwmaths_32R infvol $loop temp
-../avwmaths++ infvol $loop temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $loop volume test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $loop volume test in avwmaths++";
-fi
-rm temp*
-done
-rm infvol*
-
-ip_32R $FSLTESTDIR/common/filtered_func_data.nii.gz temp 0 -i 2000
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -inm 2000 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of ip norm test:" $output1
-limit=4
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with ip norm (-inm) test in avwmaths++";
-else echo "ip norm test within tolerance";
-fi
-rm temp*
-
-ip_32R $FSLTESTDIR/common/filtered_func_data.nii.gz temp 0 -I 2000
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz -ing 2000 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of ip global norm test:" $output1
-limit=4
-output2=`echo $output1 $limit | awk '{ print ($1 < $2) ? "passed" : "failed" }' `
-echo "$output2"
-if [ $output2 != passed ];
-then
-flag=1
-echo "Possible problem with ip global norm (-ing) test in avwmaths++";
-else echo "ip global norm test within tolerance";
-fi
-rm temp*
-
-for loop in -sub -add -mul -div -thr -uthr -max -min
-do
-avwmaths_32R $FSLTESTDIR/common/filtered_func_data.nii.gz $loop 14000 temp
-../avwmaths++ $FSLTESTDIR/common/filtered_func_data.nii.gz $loop 14000 temp1 -odt float
-avwmaths temp1 -Tmean temp2
-avwmaths temp -Tmean temp1
-avwmaths temp1 -sub temp2 -abs temp
-output1=`avwstats temp -m`
-echo "Result of $loop data test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $loop data test in avwmaths++";
-fi
-rm temp*
-done
-
-rm kernel*
-
-
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwmaths++"
-else
-echo "All comparisons zero. No problems detected with avwmaths++"
-fi
diff --git a/tests/avwmerge_test.sh b/tests/avwmerge_test.sh
deleted file mode 100755
index 54801e9..0000000
--- a/tests/avwmerge_test.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/sh
-#test 3D volume
-flag=0
-for setting in -t -x -y -z
-do
-avwmerge $setting temp $FSLTESTDIR/common/filtered_func_data.nii.gz $FSLTESTDIR/common/filtered_func_data2.nii.gz
-../avwmerge++ $setting temp2 $FSLTESTDIR/common/filtered_func_data.nii.gz $FSLTESTDIR/common/filtered_func_data2.nii.gz
-avwmaths temp2 -Tmean temp3
-avwmaths temp -Tmean temp2
-avwmaths temp3 -sub temp2 temp
-output1=`avwstats temp -m`
-echo "Result of $setting merge test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $setting test in avwmerge++";
-fi
-rm temp*
-done
-
-avwmerge -a temp $FSLTESTDIR/common//vol*
-../avwmerge++ -a temp2 $FSLTESTDIR/common/vol*
-avwmaths temp2 -Tmean temp3
-avwmaths temp -Tmean temp2
-avwmaths temp3 -sub temp2 temp
-output1=`avwstats temp -m`
-
-echo "Result of -a merge test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with -a test in avwmerge++";
-fi
-
-rm temp*
-
-
-
-
-
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwmerge++"
-else
-echo "All comparisons zero. No problems detected with avwmerge++"
-fi
\ No newline at end of file
diff --git a/tests/avwnvols_test.sh b/tests/avwnvols_test.sh
deleted file mode 100755
index 5afd986..0000000
--- a/tests/avwnvols_test.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/sh
-#test 3D volume
-flag=0
-output1=`../avwnvols++ $FSLTESTDIR/common/avg152T1_brain.img`
-output2=`avwnvols $FSLTESTDIR/common/avg152T1_brain.img`
-echo "Result of 3D nvols test:" $output1 $output2
-if [ $output1 != $output2 ];
-then
-echo "Possible problem in avwnvols++"
-flag=1
-fi
-
-
-
-#test 4D timeseries
-output1=`../avwnvols++ $FSLTESTDIR/common/filtered_func_data.nii.gz`
-output2=`avwnvols $FSLTESTDIR/common/filtered_func_data.nii.gz`
-echo "Result of 4D 100 frame nvols test:" $output1 $output2
-if [ X$output1 != X$output2 ];
-then
-echo "Possible problem in avwnvols++"
-flag=1
-fi
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "volume count discrepancy; possible problem with avwnvols++"
-else
-echo "Counts are 1 and 100. No problems detected with avwnvols++"
-fi
\ No newline at end of file
diff --git a/tests/avwroi_test.sh b/tests/avwroi_test.sh
deleted file mode 100755
index 7e4063d..0000000
--- a/tests/avwroi_test.sh
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/bin/sh
-flag_maths=0
-flag_bit=0
-#test 3D volume
-avwroi $FSLTESTDIR/common/avg152T1_brain temp1 15 20 15 20 15 20
-../avwroi++ $FSLTESTDIR/common/avg152T1_brain temp2 15 20 15 20 15 20
-cmp temp1.nii.gz temp2.nii.gz
-output2=$?
-if [ $output2 -ne 0 ]
-then
-flag_bit=1
-echo "3D roi failed bit-comparison test in avwroi++"
-fi
-avwmaths temp1 -sub temp2 temp3
-output1=`avwstats temp3 -m`
-echo "Result of 3D roi test:" $output1 $output2
-if [ $output1 != 0.000000 ];
-then
-flag_maths=1
-echo "3D roi failed math test in avwroi++";
-fi
-
-rm temp*
-
-#test 4D timeseries
-avwroi $FSLTESTDIR/common/filtered_func_data.nii.gz temp1 5 10
-../avwroi++ $FSLTESTDIR/common/filtered_func_data.nii.gz temp2 5 10
-cmp temp1.nii.gz temp2.nii.gz
-output2=$?
-if [ $output2 -ne 0 ]
-then
-flag_bit=1
-echo "4D timeseries failed bit-comparison test in avwroi++"
-fi
-avwmaths temp2 -Tmean temp3
-avwmaths temp1 -Tmean temp2
-avwmaths temp3 -sub temp2 temp1
-output1=`avwstats temp1 -m`
-echo "Result of 4D timeseries test:" $output1 $output2
-if [ $output1 != 0.000000 ];
-then
-echo "4D timeseries failed math test in avwroi++"
-flag_maths=1
-fi
-
-rm temp*
-
-#test 4D time and volume
-avwroi $FSLTESTDIR/common/filtered_func_data.nii.gz temp1 15 20 15 20 5 10 5 10
-../avwroi++ $FSLTESTDIR/common/filtered_func_data.nii.gz temp2 15 20 15 20 5 10 5 10
-cmp temp1.nii.gz temp2.nii.gz
-output2=$?
-if [ $output2 -ne 0 ]
-then
-flag_bit=1
-echo "4D timeseries and volume failed bit-comparison test in avwroi++"
-fi
-avwmaths temp2 -Tmean temp3
-avwmaths temp1 -Tmean temp2
-avwmaths temp3 -sub temp2 temp1
-output1=`avwstats temp1 -m`
-echo "Result of 4D time and volume test:" $output1 $output2
-if [ $output1 != 0.000000 ]
-then
-echo "4D timeseries and volume failed math test in avwroi++"
-flag_maths=1
-fi
-
-rm temp*
-
-echo ""
-if [ $flag_maths -ne 0 -o $flag_bit -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwroi++"
-else
-echo "All comparisons zero. No problems detected with avwroi++"
-fi
\ No newline at end of file
diff --git a/tests/avwsplit_test.sh b/tests/avwsplit_test.sh
deleted file mode 100755
index c9a9802..0000000
--- a/tests/avwsplit_test.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/sh
-flag=0
-
-for setting in -t -x -y -z
-do
-../avwsplit++ $FSLTESTDIR/common/filtered_func_data.nii.gz vol $setting
-../avwmerge $setting temp vol*
-avwmaths temp -Tmean temp2
-avwmaths $FSLTESTDIR/common/filtered_func_data.nii.gz -Tmean temp
-avwmaths temp -sub temp2 temp3
-output1=`avwstats temp3 -m`
-echo "Result of $setting split test:" $output1
-if [ $output1 != 0.000000 ];
-then
-flag=1
-echo "Possible problem with $setting test in avwsplit++";
-fi
-rm temp*
-rm vol*
-done
-
-echo ""
-if [ $flag -ne 0 ]
-then
-echo "non-zero comparison; possible problem with avwsplit"
-else
-echo "All comparisons zero. No problems detected with avwsplit"
-fi
\ No newline at end of file
diff --git a/tests/fslswapdim_test.sh b/tests/fslswapdim_test.sh
deleted file mode 100755
index f7c960e..0000000
--- a/tests/fslswapdim_test.sh
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/bin/bash
-
-## NOTE: needs links or copies of various fsl utilities to exist in ../bin at the moment (annoyingly!)
-
-mni=/home/fs0/mark/fslsrc/avwutils/tests/mni
-#mni=$FSLDIR/data/standard/MNI152_T1_2mm
-
-
-for fn in fooOLD_*.nii.gz ; do
- echo $fn
- ( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslreorient2std $mni fooRNEW )
- ( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslreorient2std $mni fooROLD )
- diff fooRNEW.nii.gz fooROLD.nii.gz
-done
-
-
-
-# num=1;
-# for aa in RL LR ; do
-# for bb in RL LR ; do
-# for cc in RL LR ; do
-# for tr1 in RLAPSI RLSIAP APSIRL APRLSI SIRLAP SIAPRL ; do
-# aaa=`echo $aa | tr R ${tr1:0:1} | tr L ${tr1:1:1}`;
-# bbb=`echo $bb | tr R ${tr1:2:1} | tr L ${tr1:3:1}`;
-# ccc=`echo $cc | tr R ${tr1:4:1} | tr L ${tr1:5:1}`;
-# echo $aaa $bbb $ccc
-# ( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooNEW_$num )
-# echo $FSLDIR
-# ( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooOLD_$num )
-# diff fooNEW_${num}.nii.gz fooOLD_${num}.nii.gz
-# num=`echo $num + 1 | bc`
-# done
-# done
-# done
-# done
-
-
-# num=1;
-# for aa in x -x ; do
-# for bb in x -x ; do
-# for cc in x -x ; do
-# for tr1 in xyz yzx zxy xzy yxz zyx ; do
-# aaa=`echo $aa | tr x ${tr1:0:1}`;
-# bbb=`echo $bb | tr x ${tr1:1:1}`;
-# ccc=`echo $cc | tr x ${tr1:2:1}`;
-# echo $aaa $bbb $ccc
-# ( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooNEW_$num )
-# echo $FSLDIR
-# ( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooOLD_$num )
-# diff fooNEW_${num}.nii.gz fooOLD_${num}.nii.gz
-# num=`echo $num + 1 | bc`
-# done
-# done
-# done
-# done
-
diff --git a/tests/header.xml b/tests/header.xml
deleted file mode 100644
index 068fb2a..0000000
--- a/tests/header.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<nifti_image
- nifti_type = 'NIFTI-1+'
- header_filename = 'filtered_func_data.nii.gz'
- image_filename = 'filtered_func_data.nii.gz'
- image_offset = '352'
- ndim = '4'
- nx = '64'
- ny = '64'
- nz = '21'
- nt = '100'
- dx = '4'
- dy = '4'
- dz = '6'
- dt = '1'
- datatype = '4'
- datatype_name = 'INT16'
- nvox = '8601600'
- nbyper = '2'
- byteorder = 'LSB_FIRST'
- cal_min = '3'
- cal_max = '25500'
- xyz_units = '2'
- xyz_units_name = 'mm'
- time_units = '8'
- time_units_name = 's'
- descrip = 'FSL3.2beta'
-/>
-
diff --git a/tests/run_alltests.sh b/tests/run_alltests.sh
deleted file mode 100755
index 0a49fe0..0000000
--- a/tests/run_alltests.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-
-echo "************************************"
-echo "Running avwroi tests"
-./avwroi_test.sh
-echo "************************************"
-echo "Running avwnvols tests"
-./avwnvols_test.sh
-echo "************************************"
-echo "Running avw2ascii tests"
-./avw2ascii_test.sh
-echo "************************************"
-echo "Running avwsplit tests"
-./avwsplit_test.sh
-echo "************************************"
-echo "Running avwcc tests"
-./avwcc_test.sh
-# echo "************************************"
-# echo "Running avwmerge tests"
-# ./avwmerge_test.sh
-echo "************************************"
-echo "Running avwinterleave tests"
-./avwinterleave_test.sh
-echo "************************************"
-echo "Running avwcpgeom tests"
-./avwcpgeom_test.sh
-echo "************************************"
-echo "Running avwhd tests"
-./avwhd_test.sh
-echo "************************************"
-echo "Running avwcreatehd tests"
-./avwcreatehd_test.sh
-echo "************************************"
-echo "Running avwmaths tests"
-./avwmaths_test.sh
-echo "************************************"
\ No newline at end of file
--
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