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neuroelf:neuroelf_pipeline

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:

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

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.

neuroelf/neuroelf_pipeline.txt · Last modified: 2016/02/03 10:34 by lydia.gibson