Ok, thanks for all 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: Thursday, December 21, 2017 2:48:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq Help
Yes, I sent the linux version, but it looks like the version you are using is up to date
On 12/21/2017 02:25 PM, Dirks, Bryce Ronald Alan wrote:
Ok thanks. I tried to use the new version of optseq2 you sent, but I keep getting a cannot execute binary file even after I have made it executable. I am using it on a macOS Sierra 10.12.6. Is it possible that the version you sent is not compatible with this OS version and if it is not do you have a different updated version?
*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:* Thursday, December 21, 2017 1:23:11 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help 30 is probably ok but you could extend to 34
On 12/21/2017 12:21 PM, Dirks, Bryce Ronald Alan wrote:
Ok, thank you. I have one more question. For our 12 sec trials what should be the size of our psywindow. We want a window big enough that it captures the entire HRF. What would be the ideal setting to do that? I originally had it set to psywindow= 0 30 1, but would that be optimal capture the entire HRF or should it be changed?
*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:* Thursday, December 21, 2017 11:43:38 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Optseq Help Oh, the message about some of the the schedules being ill-conditioned is not an error, it is just letting the user know the proportion of randomly selected schedules were bad. In this case, you have quite a large number. It should drop when you increase the ntp
On 12/21/2017 10:29 AM, Dirks, Bryce Ronald Alan wrote:
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:
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 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_ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2...
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person
to whom
it is addressed. If you believe this e-mail was sent to you in error
and the
e-mail contains patient information, please contact the Partners
Compliance
HelpLine at
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners...
. If the e-mail was sent to you in error but does not contain patient information, please contact the
sender
and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2...
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person
to whom
it is addressed. If you believe this e-mail was sent to you in error
and the
e-mail contains patient information, please contact the Partners
Compliance
HelpLine at
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners...
. If the e-mail was sent to you in error but does not contain patient information, please contact the
sender
and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2...
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person
to whom
it is addressed. If you believe this e-mail was sent to you in error
and the
e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners...
. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2...
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners...
. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg...
https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2...
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners...
. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg... https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mg... https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.