Commit 5fc0309c authored by Michael Krause's avatar Michael Krause 🎉
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matlab: add note for spm defaults

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...@@ -56,9 +56,9 @@ author = 'Michael' ...@@ -56,9 +56,9 @@ author = 'Michael'
# built documents. # built documents.
# #
# The short X.Y version. # The short X.Y version.
version = '3.6.1' version = '3.6.2'
# The full version, including alpha/beta/rc tags. # 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 # The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages. # for a list of supported languages.
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...@@ -4,6 +4,9 @@ Welcome to Tardis's documentation! ...@@ -4,6 +4,9 @@ Welcome to Tardis's documentation!
Changelog Changelog
========= =========
3.6.2 (17.12.2019)
+ new memory defaults for compiled spm12
3.6.1 (19.09.2019) 3.6.1 (19.09.2019)
+ added minimal howto for Conda + 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 ...@@ -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 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. 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 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 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 with the current image path and create a number of new batches from a single
...@@ -210,9 +209,29 @@ template: ...@@ -210,9 +209,29 @@ template:
done done
Sometimes it ***might be*** necessary to recompile the spm toolbox yourself, **SPM Memory**
for instance if you need a specific version or if you want to add external
toolboxes to SPM (e.g. cat12). 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 .. code-block:: matlab
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