Hi Cecilia - this commnd tells it to do the preprocessing (-prep), but then not to do any of the steps of the preprocessing (-no...) trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -noprior -no-isrunning
So this command won't do anything. Have you run those steps before? a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mazzetti, C. (Cecilia) <c.mazze...@donders.ru.nl> Sent: Friday, October 11, 2019 8:03:41 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA prep gets stuck in -prior 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline' External Email - Use Caution Dear all, I am trying to understand what is going on in my subjects (same problem with 5 different ones). the outputs from the first steps of trac-all seems to work fine, so I am running: trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -no-isrunning but the process gets stuck (in the log file I read something like 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline' ) which keeps going... The only outputs which seem to be created are for cst and Ilf, the others not. I am also trying to include just some tract by specifying in the configuration file: set pathlist = ( lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) but nothing seems to change.. Can I please have some assistance here? It has been days and I cannot seem to fix it.. also, I tried to run bedpost only but I receive an erro: trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -noprior -no-isrunning saying that I didn't specify any steps.. isn't bedpost a preprocessing step? also when tryingtrac-all -bedp -c config_02C.txt -no-isrunning​ nothing works... is it because the -prior steps needs to be finished? Thanks to anyone willing to help! Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen
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