neuroelf:neuroelf_pipeline
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neuroelf:neuroelf_pipeline [2014/11/15 19:17] – [Sources\MATLAB\bv_umg\ne_era] igorkagan | neuroelf:neuroelf_pipeline [2016/02/03 10:34] – [Requirements] 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 | ||
+ | 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:// | ||
+ | **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:// | ||
+ | |||
+ | Current issue that it doesn' | ||
==== Sources\MATLAB\bv_umg\ne_era ==== | ==== Sources\MATLAB\bv_umg\ne_era ==== | ||
Line 7: | Line 32: | ||
This function relies on vtc.VOITimeCourse method, which has been changed from v0.9c -> newer versions. The new method is AFT:: | This function relies on vtc.VOITimeCourse method, which has been changed from v0.9c -> newer versions. The new method is AFT:: | ||
+ | ne_era.m takes care of this: | ||
+ | <code matlab> | ||
+ | if strcmp(' | ||
+ | tc = vtc.VOITimeCourse(voi)'; | ||
+ | else | ||
+ | tc = vtc.VOITimeCourseOrig(voi)'; | ||
+ | end | ||
+ | </ | ||
+ | === ne_era_mdm.m === | ||
+ | This function extracts single-trial BOLD responses from VTCs using MDM:: |
neuroelf/neuroelf_pipeline.txt · Last modified: 2022/12/29 07:15 by 127.0.0.1