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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Colm Connolly
September 15, 2016 05:56PM
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.



Edited 3 time(s). Last edit at 09/19/2016 02:35PM by Colm Connolly.
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Subject Author Posted

in aea, are -multicost and -AddEdge incompatible?

Colm Connolly September 15, 2016 05:56PM

Re: in aea, are -multicost and -AddEdge incompatible?

Colm Connolly September 20, 2016 02:19PM

Re: in aea, are -multicost and -AddEdge incompatible?

Daniel Glen September 20, 2016 02:37PM

Re: in aea, are -multicost and -AddEdge incompatible?

debyee January 06, 2017 07:53PM