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--- biac:analysis:topup_correction [2019/02/22 17:41]
cmp12 [Prepare your input datasets]
+++ biac:analysis:topup_correction [2019/09/04 17:18]
cmp12
@@ Line 7: / Line 7: @@
 There will be two series of single timepoint EPI images.  You can grab relevant info to create the acq_params.txt files from your XML header.
-You need to calculate readout time in seconds ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ).
+You need to calculate readout time in seconds of the PEPOLAR images ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ).
 the readout time in seconds for the parameter file will be:
@@ Line 15: / Line 15: @@
 </code>
+unfortunately at this point the polarity of the images will have to be determined from visual inspection. we aren't provided enough information in the metadata to give an entry into the BXH file ( yet ).
+Here is a rough guide to help with inspection.  Take note of the eyeballs being crushed in for AP and stretched out for PA.
+{{:biac:analysis:connneuro_func.png?800|}}
-the polarity for the entry will have to be determined from the **seriesdescription**, which is typically "field map reverse polarity" or "field map regular"
 reverse will be "-1" in the acq_params.txt and regular will be "1"

Brain Imaging & Analysis Center