Hey,
I’m trying to align a lot of EPI data with poor contrast (there are no pre steady state volumes with sufficient T1 weighting to make using the LPC cost function by default viable for all subjects) with my T1 data.
To get a sense of what cost function provides the best alignment for a particular subject I’m running (from linux_openmp_64: Sep 4 2016 (Version AFNI_16.2.16)):
align_epi_anat.py -anat2epi \
-anat ${anatFile} \
-epi ${epiFile} \
-epi_base 0 \
-volreg off \
-tshift off \
-cost lpc \
-multi_cost lpa lpc+ZZ mi \
-AddEdge
When I look in the subject’s AddEdge directory the only files in there are those referring to the default LPC cost metric, For example, for one subject I get the following:
105_A.anat_unif.zp_al+orig.BRIK.gz 105_A.anat_unif.zp_al_rs+orig.HEAD _ae.ExamineList.log vr_base_ns_ec+orig.BRIK.gz
105_A.anat_unif.zp_al+orig.HEAD 105_A.anat_unif.zp_ns_e3+orig.BRIK.gz vr_base_ns_105_A.anat_unif.zp_al_rs_ec+orig.BRIK.gz vr_base_ns_ec+orig.HEAD
105_A.anat_unif.zp_al_rs_e3+orig.BRIK.gz 105_A.anat_unif.zp_ns_e3+orig.HEAD vr_base_ns_105_A.anat_unif.zp_al_rs_ec+orig.HEAD vr_base_ns+orig.BRIK.gz
105_A.anat_unif.zp_al_rs_e3+orig.HEAD 105_A.anat_unif.zp_ns_ec+orig.BRIK.gz vr_base_ns_105_A.anat_unif.zp_ns_ec+orig.BRIK.gz vr_base_ns+orig.HEAD
105_A.anat_unif.zp_al_rs_ec+orig.BRIK.gz 105_A.anat_unif.zp_ns_ec+orig.HEAD vr_base_ns_105_A.anat_unif.zp_ns_ec+orig.HEAD
105_A.anat_unif.zp_al_rs_ec+orig.HEAD 105_A.anat_unif.zp_ns+orig.BRIK.gz vr_base_ns_e3+orig.BRIK.gz
105_A.anat_unif.zp_al_rs+orig.BRIK.gz 105_A.anat_unif.zp_ns+orig.HEAD vr_base_ns_e3+orig.HEAD
Are these combinations of arguments incompatible? If so could aea be modified so that it is possible to use multicost with addedge?
I suspect the problem lies around line 3449 in align_epi_anat.py where the previous contents of AddEdge are deleted within the loop iterating over the all of the cost functions.