Differences

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--- neuroelf:neuroelf_pipeline [2014/11/15 19:01] – created igorkagan
+++ neuroelf:neuroelf_pipeline [2022/12/29 07:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ===== 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:
+<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.