Filenames do not consistently use prefix and suffix settings

[styner]

The suffix and prefix settings are not used for all files generated by Multisegpipeline. Workaround: use default setting and all is fine. If you change them, not all outputs are changes, though the "changed" output files are expected.

[j-klemm]

Tested this from the command line today and it seemed to work properly, but still waiting on the pipeline to fully finish. Will look at it with you on Monday. If it works on the CLI then perhaps it's a GUI issue. The reason I think it's working is because I changed the prefix and suffix (in data.xml) to something besides neo and NP, and the target_path in the AntsJointFusionExecution script correctly shows the correct prefix and suffix for T1 and T2 files. Perhaps it is breaking elsewhere; I am unsure of all the places to check.

[styner]

Could be a GUI issue. If that's the case, then the CLI sets/propagates certain parameter values that the GUI does not. Try to use the GUI (on an alternate output folder) and see where the scripts differ between the two runs.

[j-klemm]

Thanks for pointing that out. I think that is correct - I'm going to trace the GUI/QT settings to see if I can find where it breaks down, because the prefix/suffix are being set in multiple places, I think.

After changing the prefix and suffix to have the line
<Output-files prefix="jkprefix" suffix="jksuffix"/>
I get files in the 1.PreProcessingData dir that looks like:

-rw-r--r-- 1 jklemm rc_nirallab_psx  919009 Oct 26 14:00 jkprefix-T1-stripped-converted_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx 1835611 Oct 26 14:01 jkprefix-T1-stripped-corrected_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx  762311 Oct 26 14:00 jkprefix-T1-stripped_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx  762302 Oct 26 14:00 jkprefix-T1-stripped-positive_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx  934901 Oct 26 14:01 jkprefix-T2-stripped-converted_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx 1841431 Oct 26 14:02 jkprefix-T2-stripped-corrected_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx  775065 Oct 26 14:00 jkprefix-T2-stripped_jksuffix.nrrd
-rw-r--r-- 1 jklemm rc_nirallab_psx  775056 Oct 26 14:01 jkprefix-T2-stripped-positive_jksuffix.nrrd 

So you can see that the prefix and suffix worked correctly for the nrrd files. But it appears my pipeline cut short for some reason. Here is the entirety of jkprefix.log:

=== Preprocessing Data ===
 -> Skipped

=== Atlas Registration ===
20020 Registration... 

Are there any other logs I can look at to see what happened? I'm not sure why the prefixed files would be created in the first place if the Preprocessing Data step was skipped. (This is probably a dev issue unrelated to the prefixing and suffixing but I'm posting it here because it shows that setting the prefix with the CLI appears to be working).

[styner]

Only data that has not yet been computed (and thus, for which there is no output files), will be processed/computed. If a corresponding output file exists, then that step is skipped.

Also, the issue is not that the output files would be not correctly adjusted to the prefix and suffix setting, but rather that one of the scripts (AntsJointFusionExecution script) did not adjust its pathnames for some of the prior step's output.