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neuroelf:neuroelf_pipeline [2014/11/15 19:05]
igorkagan
neuroelf:neuroelf_pipeline [2016/02/03 10:30]
lydia.gibson
Line 1: Line 1:
 ===== 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
  
 +==== 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 ==== ==== Sources\MATLAB\bv_umg\ne_era ====
 === ne_era.m === === 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.
neuroelf/neuroelf_pipeline.txt · Last modified: 2016/02/03 10:34 by lydia.gibson