External Email - Use Caution
Hi FS Team,
We've tried running preproc-sess using a custom instem, but it fails at
rawfunc2surf-sess.
From parsing the code a bit, it appears that while most of the x-sess
scripts called in preproc-sess pass their respective outstem's as the
instem to the subsequent function, rawfunc2sess is never given an explicit
instem and instead builds up its instem based on assumptions from the
provided flags. So while our stc-sess outstem according to the log was
"fmcpricor.odd" (based on a custom instem "fmcpricor", followed by no
mc-sess, and stc-sess), our rawfunc2surf-sess instem defaulted to
"fmcpr.odd".
Similarly it will also miss some other flags given to preproc-sess. For
example, the -nomc flag passed to preproc-sess will not effect
rawfunc2surf-sess instem, as it adds "mcpr" to the proposed instem based on
the -per-run flag, and does not take the -nomc flag into account. So any
preproc-sess calls using -nomc will fail at rawfunc2surf-sess.
Am I interpreting this correctly? My assumption is that I will either need
to add instem passing to my local preproc-sess file, or otherwise call each
of the x-sess scripts directly in my own script rather than using
preproc-sess?
Thanks,
Jacob Matthews
MRI Specialist
Rotman Research Institute
Baycrest Hospital
416-785-2500 ext. 3322
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