add more infos for reproducibility

Signed-off-by: Stephen L. <[email protected]>

Author: lrq3000

.gitattributes

@@ -0,0 +1 @@
+*.zip filter=lfs diff=lfs merge=lfs -text

README.md

@@ -9,6 +9,8 @@ All tools are licensed under MIT (but not necessarily the required/optional libr
 
 The rest of this document will describe some of the tool's purpose, usage and linked libraries. More documentation will be written in the future (maybe). In any case, literate programming is extensively used, so that you can expect lots of comments inside the scripts itself, so that they should be useable without any external documentation.
 
+The directory "external" contains external packages to ease reproducibility of our scripts by providing the exact same revisions of the packages we used.
+
 ## pathmatcher: Regular Expression Path Matcher
 
 ### Description
@@ -21,7 +23,7 @@ If you happen to know this situation, this tool might help you: just specify a r
 
 This application can also be used as a Python module, so that you can include it in a pipeline to (semi-)automate repetitive stuff, like selecting the appropriate files to open in your favorite tool like SPM. For an exemple, see the script `reorient_pipeline` at the root of this repository.
 
-Runs on Python 2.7.11, but uses good standards to ensure easy conversion to Python 3 in case you really need it.
+Runs on Python 2.7.15, but uses good standards to ensure easy conversion to Python 3 in case you really need it.
 
 If you are not experienced with [regular expressions](http://regexone.com/), you can use online tools such as [Pythex](http://pythex.org/) to instantly test your regexp.
 

preprocessing/smri/README.txt

@@ -1 +1,3 @@
 Structural MRI voxel-based morphometry with DARTEL analysis pipeline using VBM8 and SPM8 or CAT12 and SPM12. The entry script is vbm_script_preproc_csg.m (requires MATLAB) and also needs Python with PILLOW if you want to automatically generate result images. This pipeline is also interesting to see how it is possible to fully automate graphical results generation in SPM.
+
+Please also use the exact SPM12 and CAT12 versions that are specified in the header of vbm_script_preproc_csg.m (they are available in the folder external).

preprocessing/smri/vbm_script_preproc_csg.m

@@ -6,9 +6,13 @@ function vbm_script_preproc_csg()
 % VBM with DARTEL preprocessing will be done and also 2nd-level analysis SPM.mat of one patient/subject against a group of controls. A picture of the results using the voxel-wise thresholding of your choice can be generated for each subject.
 %
 % You need to have installed the following libraries prior to launching this script:
-% * SPM8 + VBM8 (inside spm/toolbox folder) OR SPM12 + CAT12 (Geodesic Shooting, not DARTEL, r1434 | gaser | 2019-02-28 11:31:30) (inside spm/toolbox folder)
+% * SPM8 + VBM8 (inside spm/toolbox folder) OR SPM12 + CAT12 (Geodesic Shooting, not DARTEL) (with cat12 inside spm/toolbox folder)
 % Note: please enable expertgui (set to 1) in cat_defaults.m to see all the options used here.
 %
+% Exact versioning:
+% * SPM12 Version 7487 (SPM12) 14-Nov-18 (from spm/Contents.m or by typing [a, b] = spm('Ver))
+% * CAT12 r1434 | gaser | 2019-02-28 11:31:30 (from cat12/CHANGES.txt)
+%
 % Also you need to use a fully compatible MATLAB version with SPM8. It was successfully tested on Matlab2011a and Matlab2013a, but failed with MATLAB 2016a. However, it successfully worked with MATLAB 2018a by modifying spm_render.m lines 260-261, change:
 %    load('Split');
 %    colormap(split);
@@ -18,7 +22,7 @@ function vbm_script_preproc_csg()
 % You also need Python (and add it to the PATH! Must be callable from cmd.exe with a simple "python" command) and PILLOW (not PIL! Just do `conda install pillow` or `pip install pillow`) to generate the final stitched image, but if you want to do it yourself it is not needed.
 %
 % STEPHEN KARL LARROQUE
-% v1.3.0
+% v1.3.1
 % First version on: 2017-01-24 (first version of script based on batch from predecessors)
 % 2017-2019
 % LICENSE: MIT