Current BCD Eye Center Manual Intervention Method

##1 make a directory adjacent to ANONRAW for the MANUAL_FIX.

cd /Shared/nopoulos/structural/oz_MR/S104/S104-v1/ mkdir MANUAL_FIX cd MANUAL_FIX

##2 Copy the failed “EMSP* files from the failied BCD ron to the MANUAL_FIX directory”

cp /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S104_S104-v1/LandmarkInitialize/BCD/EMSP.nrrd S104_S104-v1_T1_EYES_FIXED.nrrd

cp /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S104_S104-v1/LandmarkInitialize/BCD/EMSP.fcsv EMSP.fcsv

##3 In slicer version 4.8.1 (October 2017 release) open the .nrrd and .fcsv files

NOTE the .nrrd file has a special extra header meta-data line that points to the EMSP.fcsv file

In slicer move the RE and LE fiducial to the center of the eyes

Save the fcsv file only, then open the fcsv file to ensure that the points have been changed

##4 Creat a _noDenoise file to indicate that previous steps need to be skipped. touch S104_S104-v1_T1_EYES_FIXED.nrrd_noDenoise

##5 Update .csv file to reflect new inputs ie "OZ","S106","S106-v1","{'T1-30':['/Shared/nopoulos/structural/oz_MR/S106/S106-v1/MANUAL_FIX/S106_S106-v1_T1_EYES_FIXED.nrrd']}"