Hi Rebecca,

The censored displacement just considers time points that were not removed, those that are still in the time series after censoring. It is more useful, since those are the time points that will be considered in the regression.

The gen_ss_review_table.py commands should not go into each subject's directory. The input to that command is generally a list of out.ss_review files across all subjects at once. One command might have out.ss_review files for 200 subjects.

The output from gen_ss_review_table.py might be just a spreadsheet (one row per subject, one column per field entry), or it might be a list of subjects that could be dropped because one or more values are too extreme.


Regarding your errors, the one with .../$subj/... "file not found" is odd. That suggests there are single quotes in use in the script, which I do not see in the posting. Since $subj (the actual variable reference) is in the text output, the shell must be being blocked from using its value instead.

The second error could be for the same reason, it is hard to say. But if you replaced the gen_ss command (or preceded it) with something like:

ls -ld $sdir

it would presumably show a "file not found" error. In any case, it is not seeing $sdir.


Regarding the last command, that -infiles option should read more like:

-infiles $ALL_SUBJECTS/sub*/*.results/out.ss*.txt

That would include all subjects in the input.

Does that seem reasonable?

- rick