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neuroelf:neuroelf_pipeline [2014/11/15 19:20] – [Sources\MATLAB\bv_umg\ne_era] igorkaganneuroelf:neuroelf_pipeline [2016/02/03 10:30] lydia.gibson
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 ===== 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).  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> <code matlab>
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 </code> </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: 2022/12/29 07:15 by 127.0.0.1