That is the complete terminal and thank you for your help!
Bryce Dirks Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website: http://www.psy.miami.edu/bccl/ Phone: (305)284-3286
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, December 20, 2017 6:38:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq Help
send me the full terminal output that includes the error
On 12/20/2017 05:05 PM, Dirks, Bryce Ronald Alan wrote:
*Bryce Dirks* Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miam... Phone:_ (305)284-3286_
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Wednesday, December 20, 2017 4:44:40 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help Run
optseq2 --all-info
and send the result. I think you may be using an older version. I've put the newest version here
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
On 12/20/2017 04:26 PM, Dirks, Bryce Ronald Alan wrote:
We are not using freesurfer, but just the optseq2 unix script.
*Bryce Dirks* Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miam...
Phone:_ (305)284-3286_
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Wednesday, December 20, 2017 3:40:48 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help Can you send me the terminal output? I ran this command and did not receive any errors using v6
optseq2 --ntp 180 --tr 2 --psdwin 0 30 1 --ev flexibility 12 10 --ev control 12 10 --nsearch 10000 --nkeep 3 --o cFIST_10trials8s_Run1
what version of FS are you running?
On 12/20/2017 02:29 PM, Dirks, Bryce Ronald Alan wrote:
I also tried reducing the window and that removed the error. I also only get the error on a subset of the schedule so if we keep the top 3 would they /not/ be ill-conditioned?
*Bryce Dirks* Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miam...
Phone:_ (305)284-3286_
*From:* Dirks, Bryce Ronald Alan *Sent:* Wednesday, December 20, 2017 11:44:03 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help
I added 120 to the ntp make ntp=300, but still got the same error. I also tried running a ntp=360 and got the same ill-condtioned
statement.
*Bryce Dirks* Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miam...
Phone:_ (305)284-3286_
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Tuesday, December 19, 2017 6:21:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help You need to include some time for fixation. Ie, your total run time is 180*2=360 sec. The total stimulation time is 12*10*3 = 360 sec.
You need
to increase the length of the fmRI run (or reduce the total number of stimuli). Usually I include as much fixation as any other
condition. In
this case, that would be 12*10=120 sec. So try adding 120 sec (ie, incrase --ntp 180) and re-run
On 12/19/2017 05:21 PM, Dirks, Bryce Ronald Alan wrote:
Hello,
I am trying to create the optseq for a cognitive flexibility experiment we are conducting. It consists of 10 flexibility, 10 control, and 10 fixation trials. The flexibility and control trials are 12 seconds long. Our TR= 2s. We want to ensure our trial onsets are not time-locked to our TR. We are also unsure how long our response window should be given our rather long trial duration
(12s).
The code below is what I have made to try to do this and I keep getting that the schedules were ill-conditioned. Any information on how to resolve this error is appreciated!
/./optseq2 --ntp 180 --tr 2 --psdwin 0 30 1 --ev flexibility 12 10 --ev control 12 10 --nsearch 10000 --nkeep 3 --o
cFIST_10trials8s_Run1/
//
Thank you,
*Bryce Dirks* Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miam...
Phone:_ (305)284-3286_
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