neuroelf:neuroelf_pipeline
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neuroelf:neuroelf_pipeline [2014/11/15 19:20] igorkagan [Sources\MATLAB\bv_umg\ne_era] |
neuroelf:neuroelf_pipeline [2016/02/03 10:32] lydia.gibson [Requirements] |
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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 ==== | ||
| Line 17: | Line 42: | ||
| </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: 2016/02/03 10:34 by lydia.gibson
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