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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mazzetti, C. (Cecilia) C.Mazzetti@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
freesurfer@nmr.mgh.harvard.edu
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Mazzetti, C. (Cecilia) -
Yendiki, Anastasia