===== NeuroElf pipeline ======
==== Requirements ====
MATLAB 64bit\\ NeuroElf v1.0\\ BrainVoyager 2.4\\
Following folders of Dropbox\DAG\Sources\bv_umg on your MATLAB path list:
  * _4NeuroElf
  * monkeypsych_mat2prt
  * ne_era
  * ne_pipeline_converged
  * ne_prt2avg (add the script for your dataset)
Following folders of Dropbox\DAG\Sources on your MATLAB path list:
  * roi
  * NaN
  * Igtools
See also [[neuroelf_resources]]
==== ne_fmriquality.m ====
modification of original fmriquality with options for outliers analysis IK 2014

does not work with NE v1.0 (many @neuroelf\private function that are used inside are missing)

http://neuroelf.net/wiki/doku.php?id=fmriquality : 
**Finally, at the moment, the “problem detection” thresholds (to mark a volume as outliers) are fixed, but are likely to change in a future version.** 


==== Create VTC ====

http://neuroelf.net/wiki/doku.php?id=vmr.createvtc#method_reference_vmrhelp_createvtc

Current issue that it doesn't work with monkey data - sag, cor and axi planes are confused in the resulting VTC.

==== Sources\MATLAB\bv_umg\ne_era ====
=== ne_era.m ===
This function relies on vtc.VOITimeCourse method, which has been changed from v0.9c -> newer versions. The new method is AFT::VOITimeCourse, in versions v0.9d and 1.0, this method works only with TAL vois. The method vtc.VOITimeCourseOrig is kept for backward compatibility (works with both BV and TAL vois). 

ne_era.m takes care of this:

<code matlab>
	if strcmp('0.9c',v) || strcmp(voi.ReferenceSpace,'TAL'),
		tc = vtc.VOITimeCourse(voi)'; % each row - one roi tc
	else
		tc = vtc.VOITimeCourseOrig(voi)'; 
	end
</code>

=== ne_era_mdm.m ===
This function extracts single-trial BOLD responses from VTCs using MDM::VOITimeCourses for each VOI specified in a given VOI file. If necessary, VOIs in BV native space are automatically converted into TAL space using ne_voicoord2tal.m.