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--- biac:analysis:physiological [2013/04/02 19:40]
petty [FSL Feat]
+++ biac:analysis:physiological [2022/01/18 16:09]
cmp12
@@ Line 1: / Line 1: @@
 ====== Physiological Correction Methods ======
+===== Generate resampled TSV from raw GE physio files automatically copied from the scanners  =====
+<code>
+[cmp12@blade17 20211218_03399]$ /usr/local/packages/biacpython/bin/convert_GEphysio.py --help
+usage: convert_GEphysio.py [-h] --xmlh XMLFNAME [--json JSONFNAME] --physdir
+                           PHYSDIR [--bidsout] [--afnislicetime]
+                           [--delay DELAYTIME]
+create 100Hz resampled TSV from raw GE physio data
+optional arguments:
+  -h, --help         show this help message and exit
+  --xmlh XMLFNAME    BXH data
+  --json JSONFNAME   JSON data
+  --physdir PHYSDIR  physio directory
+  --bidsout          write BIDS specific TSV data and json sidecar
+  --afnislicetime    write AFNI slicetiming 1D files for RetroTS and tshift
+  --delay DELAYTIME  time past ending time of functional to end search for
+                     matching physio files
+</code>
+===== CIGAL specific =====
 Currently this assumes that you have recorded your physiological responses through Cigal.  Also, these types of corrections should be done **before** any type of slice-time correction or pre-processing.

Brain Imaging & Analysis Center