hello experts!
I’m at step 16 of the multi-tissue fixel pipeline (“Assign subject fixels to template fixels”) and up until now everything has been pretty smooth. For >120 datasets I’m parallel-processing the pipeline on a cluster (when appropriate) and am now getting errors for ~10% of the subjects, which is strange to me because it’s usually all or none that break. More specifically, I’m getting 2 errors, the main one is:
fixelcorrespondence: [ERROR] output fixel directory "../template/fd" already contains index file, which is not the same as the expected output
That is correct: …/template/fd already contains (one) index.mif and one directions.mif, but why would this only break on some subjects?
Also, for 1 subject I’m getting:
fixelcorrespondence: [ERROR] invalid first line for key/value file "fixel_in_templ_spc_subjectname/fd.mif" (expected "mrtrix image")
and for another subject it’s the same basic error but referring to the directions.mif instead of the fd.mif.
However, both of those files are there for both subjects so i’m utterly confused there, too.
Finally, the actual command I submitted to the job array is simply:
fixelcorrespondence -nthreads 8 fixel_in_templ_spc_${subj}/fd.mif ../template/fixel_mask ../template/fd sfix_to_templfix_${subj}.mif
Any help troubleshooting this will be super appreciated!
-Sam