matlab: add note for spm defaults

conf.py

@@ -56,9 +56,9 @@ author = 'Michael'
 # built documents.
 #
 # The short X.Y version.
-version = '3.6.1'
+version = '3.6.2'
 # The full version, including alpha/beta/rc tags.
-release = '3.6.0'
+release = '3.6.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

index.rst

@@ -4,6 +4,9 @@ Welcome to Tardis's documentation!
 Changelog
 =========
 
+3.6.2 (17.12.2019)
+  + new memory defaults for compiled spm12
+
 3.6.1 (19.09.2019)
   + added minimal howto for Conda
 

software/matlab.rst

@@ -191,7 +191,6 @@ Usually users are exporting a number of batch files with the spm gui on their
 local machine, change the paths to reflect the names on the Tardis and then
 call :program:`run_spm12.sh` with the **batch** parameter for each batch file.
 
-
 Example: segmentation for a number of nifti images. The file batch.template
 contains the string :file:`%%IMAGE%%` as a placeholder so we can easily replace it
 with the current image path and create a number of new batches from a single
@@ -210,9 +209,29 @@ template:
    done
 
 
-Sometimes it ***might be*** necessary to recompile the spm toolbox yourself,
-for instance if you need a specific version or if you want to add external
-toolboxes to SPM (e.g. cat12).
+**SPM Memory**
+
+By default, SPM uses very conservative memory settings. Combined with large
+time-series data and a networked file system this can quickly result in
+inefficient I/O patterns due to unnecessary data chunking and hasty saving of
+intermediate results. (thank you Nir Moneta for finding and reporting this!)
+
+For that reason, our pre-compiled SPM modules now contain these new default values:
+
+.. code-block:: matlab
+
+    global defaults;
+    defaults.stats.maxmem   = 2^32; % increases chunk size
+    defaults.stats.resmem   = true; % do not save intermediate steps
+
+If you need different defaults (possibly up to `2^38` / 256GB ), you need to
+include a custom :file:`spm_my_defaults.m` and re-compile SPM12.
+
+**(Re-)Compiling**
+
+Sometimes it *might be* necessary to recompile the spm toolbox yourself,
+for instance if you need a specific version, if you want to add external
+toolboxes to SPM (e.g. cat12) or if you need to change some spm defaults.
 
 .. code-block:: matlab