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README.md

@@ -1,12 +1,20 @@
-### SnPM: Statistical nonParametric Mapping
+## SnPM: Statistical nonParametric Mapping
 
-The <b>S</b>tatistical <b>n</b>on-<b>P</b>arametric <b>M</b>apping (SnPM) toolbox provides an extensible framework for voxel level non-parametric permutation/randomisation tests of functional Neuroimaging experiments with independent observations. 
+The Statistical non-Parametric Mapping (SnPM) toolbox provides an extensible framework for voxel level non-parametric permutation/randomisation tests of functional Neuroimaging experiments with independent observations. 
 
 The SnPM toolbox provides an alternative to the Statistics section of [SPM](http://www.fil.ion.ucl.ac.uk/spm/). SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomisation/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions.
 
-#### Testing
+**More information at: www.warwick.ac.uk/snpm**
 
-##### Initial set up 
+ - [Getting started](http://www.warwick.ac.uk/snpm/man)
+ - [fMRI example](http://www.warwick.ac.uk/snpm/man/exnew)
+ - [PET example](http://www.warwick.ac.uk/snpm/man/ex)
+ - [Download](http://www.warwick.ac.uk/snpm/snpmreg)
+
+
+### Testing
+
+#### Initial set up 
 The first time you run the tests, you will first have to create a set of ground truth data and a file named `snpm_test_config.m` containing the reference SnPM version you used to compute the ground truth and the path to the ground truth folder. For example:
 ```
 global testDataDir;
@@ -15,25 +23,25 @@ global SnPMrefVersion;
 SnPMrefVersion = 'SnPM8';
 ```
 
-##### Run the test suite
+#### Run the test suite
 Then, the tests can be started (from the test data folder) with:
 ```
 import matlab.unittest.TestSuite;
 suite = TestSuite.fromFolder(fullfile(spm_str_manip(which('snpm'), 'h'), 'test'));
 result = run(suite);
 ```
 
-##### Run a single test
+#### Run a single test
 ```
 run(test_oneSample, 'test_onesample_1')
 ```
 
-#### SnPM13: Bugs & Fixes
+### SnPM13: Bugs & Fixes
 
 This section describes the bugs that have been reported, along with the appropriate fixes. 
 Updated versions of appropriate SnPM functions are available at [snpm13_updates](http://warwick.ac.uk/snpm/distribution/snpm13_updates)
 
-#####  SnPM 13.1.04
+####  SnPM 13.1.04
 * snpm
 SnPM version 13.1.04
 
@@ -69,14 +77,14 @@ test_onesub_twocondrepl, test_twoSample, test_twosample_twocond
 Test in command-line mode with no shuffling for the random seed, using new rng
  syntax.
 
-#####  Updates from SnPM 13.1.03
+####  Updates from SnPM 13.1.03
 * snpm
 SnPM version 13.1.03
 
 * snpm_pi_PairT
 Now allows more than 52 subjects, as previously that would generate a "Maximum variable size allowed by the program" error message.
 
-#####  Updates from SnPM 13.1.02
+####  Updates from SnPM 13.1.02
 * snpm
 SnPM version 13.1.02
 
@@ -86,30 +94,30 @@ Update contrast display for compatibility with Matlab R2014b.
 * generic_test_snpm
 Updates affecting tests only.
 
-#####  Updates from SnPM 13.1.01
+####  Updates from SnPM 13.1.01
 * snpm
 SnPM version 13.1.01
 
 * snpm_pp
 Check that 'Locs_vox' is integer according to a pre-defined tolerance level (as in snpm_cp).
 
-#####  Updates from SnPM13.1.00
+####  Updates from SnPM13.1.00
 * snpm_cp, snpm_pp, generic_test_snpm, test_oneSample
 Cluster-forming threshold defined by a P-value are now extended to pseudo-T statistic (with variance smoothing). The Z-score corresponding to the selected P-value is used as an approximation of pseudo-T values.
 
-#####  Updates from SnPM13.0.14
+####  Updates from SnPM13.0.14
 * snpm_bch_ui_Corr, snpm_bch_ui_Corr1S, snpm_pi_Corr, snpm_pi_Corr1S, test_multisubsimpleregression, test_onesub_regression
 Introduce nuisance covariates in simple-subject and multi-subject regressions.
 
-#####  Updates from SnPM13.0.13
+####  Updates from SnPM13.0.13
 * snpm_combo_pp
 Fix: Set bNeg to 0 for F-tests.
 
-#####  Updates from SnPM13.0.12
+####  Updates from SnPM13.0.12
 * snpm_pi_OneSampT
 Fix: Added new random mode for sampling of sign flips (Above 53 scans the binary-coding fails as Matlab's double significand runs out of precision).
 
-#####  Updates from SnPM13.0.11
+####  Updates from SnPM13.0.11
 * snpm_ui
 Fix: When relative thresholding is set, then global calculation (user defined or mean) must be computed.
 
@@ -119,22 +127,22 @@ Fix: Unbalanced two-sample tests were wrongly aborted.
 * test_multisubpaired2cond, test_oneSample, test_twoSample, test_twosample_twocond
 Updates affecting tests only.
 
-#####  Updates from SnPM13.0.10 
+####  Updates from SnPM13.0.10 
 * snpm_ui
 Fix: ANCOVA normalisation (with an image presenting negative mean using spm_globals).
 
-#####  Updates from SnPM13.09
+####  Updates from SnPM13.09
 * snpm_cp
 Increase tolerance in checking that 'Locs_vox' is integer.
 
-#####  Updates from SnPM13.08
+####  Updates from SnPM13.08
 * snpm_cp, spm_append_96
 Display warning message if SnPM_ST file becomes very large. Display more meaningful error message when Locs_vox is not interger.
 
 * snpm_pp
 Display warning message if SnPM_ST can not be loaded.
 
-#####  Updates from SnPM13.07
+####  Updates from SnPM13.07
 * snpm
 For backward-compatibility, open SPM batch window and display where to find SnPM tools when 'snpm' in called at the Matlab prompt.
 
@@ -144,14 +152,14 @@ Fix: slow cluster inference with variance smoothing.
 * generic_test_snpm, test_oneSample, test_twoSample
 Updates affecting tests only.
 
-#####  Updates from SnPM13.06
+####  Updates from SnPM13.06
 * snpm_ui
 Apply user-defined scaling.
 
 * generic_test_snpm, test_oneSample, test_onesub_twocondrepl, test_twoSample
 Updates affecting tests only.
 
-#####  Updates from SnPM13.05
+####  Updates from SnPM13.05
 * snpm_STcalc
 Cluster labels from spm_max are not necessarily continuous.
 
@@ -161,15 +169,15 @@ Fix: if number of requested permutations is equal to the maximum number of possi
 * snpm_pi_TwoSampTss, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT
 Compute possible permutations (PiCond) in a more efficient way to avoid potential memory faults for large groups.
 
-#####  Updates from SnPM13.04
+####  Updates from SnPM13.04
 * snpm_ui
 Apply absolute and relative masking.
 
-#####  Updates from SnPM13.03
+####  Updates from SnPM13.03
 * snpm_pi_TwoSampT
 Compute possible permutations (PiCond) in a more efficient way to avoid potential memory faults for large groups.
 
-#####  Updates from SnPM13.02
+####  Updates from SnPM13.02
 * snpm_pp
 Fix: if the extension is missing in the provided result file name, use .nii by default.
 Use NaNs in thresholded map background instead of zeros.
@@ -183,7 +191,7 @@ Minor update in the display.
 * test/
 Miror corrections affecting tests procedure only.
 
-#####  Updates from SnPM13.01
+####  Updates from SnPM13.01
 * snpm_cp 
 Synopsis: When half the permutations are computed (i.e. bhPerms is true) and StartPerm is 2 then the initial number of permutation could be 2 depending on sign of T0.