z2labelmap 1.1.8

Convert lh/rh z-score vector to FreeSurfer labelmap

pl-z2labelmap
=============

.. image:: https://badge.fury.io/py/z2labelmap.svg
:target: https://badge.fury.io/py/z2labelmap

.. image:: https://travis-ci.org/FNNDSC/z2labelmap.svg?branch=master
:target: https://travis-ci.org/FNNDSC/z2labelmap

.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
:target: https://badge.fury.io/py/pl-z2labelmap

.. contents:: Table of Contents


Abstract
--------

``zlabelmap.py`` generates FreeSurfer labelmaps from z-score vector files. These labelmap files are used by FreeSurfer to color-code parcellated brain regions. By calculating a z-score to labelmap transform, we are able to show a heat map, hightlight brain regions that differ from some comparative reference, as shown below

.. image:: https://github.com/FNNDSC/pl-z2labelmap/wiki/images/subj1-heatmap/frame126.png

where positive volume deviations of a parcellated brain region are shown in red (i.e. the subject had a larger volume in that area than the reference), and negative volume deviations are shown in blue (i.e. the subject had a smaller volume in that area than reference).

*Note that this are randomly generated z-scores purely for illustrative purposes*.

Essentially the script consumes an input text vector file of

.. code::

<str_structureName> <float_lh_zScore> <float_rh_zScore>

for example,

.. code::

G_and_S_frontomargin ,1.254318450576827,-0.8663546810093861
G_and_S_occipital_inf ,1.0823728865077271,-0.7703944006354377
G_and_S_paracentral ,0.20767669866335847,2.9023126278939912
G_and_S_subcentral ,2.395503357157743,-1.4966482475891556
G_and_S_transv_frontopol ,-1.7849555258577423,-2.461419463760234
G_and_S_cingul-Ant ,-2.3831737860960382,1.1892593438667625
G_and_S_cingul-Mid-Ant ,0.03381695289572084,-0.7909116233500506
G_and_S_cingul-Mid-Post ,-2.4096082230335485,1.166457973597625
...
...
S_postcentral ,1.3277159068067768,-1.4042773812503526
S_precentral-inf-part ,-1.9467169777576718,1.7216636236995733
S_precentral-sup-part ,0.764673539853991,2.1081570332369504
S_suborbital ,0.522368665639954,-2.3593237820349007
S_subparietal ,-0.14697262729901928,-2.2116605141889094
S_temporal_inf ,-1.8442944920810271,-0.6895142771486307
S_temporal_sup ,-1.8645248463693804,2.740099589311164
S_temporal_transverse ,-2.4244451521560073,2.286596403222344

and creates a FreeSurfer labelmap where ``<str_structureName>`` colors correspond to the z-score (normalized between 0 and 255).

Currently, only the ``aparc.a2009s`` FreeSurfer segmentation is fully supported, however future parcellation support is planned.

Negative z-scores and positive z-scores are treated in the same manner but have sign-specific color specifications. Positive and negative z-Scores can be assigned some combination of the chars ``RGB`` to indicate which color dimension will reflect the z-Score. For example, a

.. code::

--posColor R --negColor RG

will assign positive z-scores shades of ``red`` and negative z-scores shades of ``yellow`` (Red + Green = Yellow).



Synopsis
--------

.. code::

python z2labelmap.py \
[-v <level>] [--verbosity <level>] \
[--random] \
[-p <f_posRange>] [--posRange <f_posRange>] \
[-n <f_negRange>] [--negRange <f_negRange>] \
[-P <'RGB'>] [--posColor <'RGB'>] \
[-N <'RGB'> [--negColor <'RGB'>] \
[-s <f_scaleRange>] [--scaleRange <f_scaleRange>] \
[-l <f_lowerFilter>] [--lowerFilter <f_lowerFilter>] \
[-u <f_upperFilter>] [--upperFilter <f_upperFilter>] \
[-z <zFile>] [--zFile <zFile>] \
[--version] \
[--man] \
[--meta] \
<inputDir> \
<outputDir>

Run
----

This ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image.

Using PyPI
~~~~~~~~~~

To run from PyPI, simply do a

.. code:: bash

pip install z2labelmap

and run with

.. code:: bash

z2labelmap.py --man /tmp /tmp

to get inline help.


Using ``docker run``
~~~~~~~~~~~~~~~~~~~~

To run using ``docker``, be sure to assign an "input" directory to ``/incoming`` and an output directory to ``/outgoing``. *Make sure that the* ``$(pwd)/out`` *directory is world writable!*

Now, prefix all calls with

.. code:: bash

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-z2labelmap z2labelmap.py \

Thus, getting inline help is:

.. code:: bash

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-z2labelmap z2labelmap.py \
--man \
/incoming /outgoing

Examples
--------

Create a sample/random z-score file and analyze
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* In the absense of an actual z-score file, the script can create one. This can then be used in subsequent analysis:

.. code::

mkdir in out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-z2labelmap z2labelmap.py \
--random \
--posRange 3.0 --negRange -3.0 \
/incoming /outgoing

or without docker

.. code::

mkdir in out
z2labelmap.py \
--random \
--posRange 3.0 --negRange -3.0 \
/in /out


In this example, z-scores range between 0.0 and (+/-) 3.0.

Control relative brightness and lower filter low z-scores from final labelmap
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* To analyze a file already located at ``in/zfile.csv``, apply a ``scaleRange`` and also filter out the lower 80\% of z-scores:

.. code::

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-z2labelmap z2labelmap.py \
--scaleRange 2.0 --lowerFilter 0.8 \
--negColor B --posColor R \
/incoming /outgoing

This assumes a file called 'zfile.csv' in the <inputDirectory> that ranges in z-score between 0.0 and 3.0, and uses the --scaleRange to reduce the apparent brightness of the map by 50 percent. Furthermore, the lower 80 percent of z-scores are removed (this has the effect of only showing the brightest 20 percent of zscores).

Using the above referenced z-score file, this results in:

.. code::

.. code::



0 Unknown 0 0 0 0
11101 lh-G_and_S_frontomargin 0 0 0 0
11102 lh-G_and_S_occipital_inf 0 0 0 0
11103 lh-G_and_S_paracentral 0 0 0 0
11104 lh-G_and_S_subcentral 103 0 0 0
11105 lh-G_and_S_transv_frontopol 0 0 0 0
11106 lh-G_and_S_cingul-Ant 0 0 110 0
11107 lh-G_and_S_cingul-Mid-Ant 0 0 0 0
11108 lh-G_and_S_cingul-Mid-Post 0 0 111 0
...
...
12167 rh-S_postcentral 0 0 0 0
12168 rh-S_precentral-inf-part 0 0 0 0
12169 rh-S_precentral-sup-part 0 0 0 0
12170 rh-S_suborbital 0 0 110 0
12171 rh-S_subparietal 0 0 103 0
12172 rh-S_temporal_inf 0 0 0 0
12173 rh-S_temporal_sup 119 0 0 0
12174 rh-S_temporal_transverse 0 0 0 0

Command line arguments
----------------------

.. code::

<inputDir>
Required argument.
Input directory for plugin.

<outputDir>
Required argument.
Output directory for plugin.

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--random]
If specified, generate a z-score file based on <posRange> and <negRange>.

[-p <f_posRange>] [--posRange <f_posRange>]
Positive range for random max deviation generation.

[-n <f_negRange>] [--negRange <f_negRange>]
Negative range for random max deviation generation.

[-P <'RGB'>] [--posColor <'RGB'>]
Some combination of 'R', 'G', B' for positive heat.

[-N <'RGB'> [--negColor <'RGB'>]
Some combination of 'R', 'G', B' for negative heat.

[-s <f_scaleRange>] [--scaleRange <f_scaleRange>]
Scale range for normalization. This has the effect of controlling the
brightness of the map. For example, if this 1.5 the effect
is increase the apparent range by 50% which darkens all colors values.

[-l <f_lowerFilter>] [--lowerFilter <f_lowerFilter>]
Filter all z-scores below (normalized) <lowerFilter> to 0.0.

[-u <f_upperFilter>] [--upperFilter <f_upperFilter>]
Filter all z-scores above (normalized) <upperFilter> to 0.0.

[-z <zFile>] [--zFile <zFile>]
z-score file to read (relative to input directory). Defaults to 'zfile.csv'.

[--version]
If specified, print version number.

[--man]
If specified, print (this) man page.

[--meta]
If specified, print plugin meta data.