Commit 5fc0309c authored by Michael Krause's avatar Michael Krause 🎉
Browse files

matlab: add note for spm defaults

parent 805015b8
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......@@ -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.
......
......@@ -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
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......@@ -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
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