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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