By default, optseq2 assumes that you want to perform an FIR analysis
where you get an average for each post-stimulus time point so that you
can create a waveform. This is in contrast to assuming the shape to the
hemodyn respnse where you only estimate a single value (the amplitude).
By
External Email - Use Caution
Dear Developers,
I am planning to run PVT (psychomotor vigilance task) in fMRI using event
related design. This is an extremely simple reaction time task: participant
has to respond to the appeared geometric shape as quickly as possible. The
key
You are probably interested in the power (ie, "can I detect an effect
with this many trials scheduled in this way?"). It is not possible to
answer this question without an effect size. Having said that, I
generally feel comfortable when the VRF is 20-40. Note that this assumes
an FIR (not
On 7/15/2019 12:50 PM, Tugce Duran wrote:
External Email - Use Caution
Hi Dr. Greve,
I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI
task for our study.
There are 80 face-name pairs that we will use and the duration can be between
3.5 and 4.75 secs. I
External Email - Use Caution
Hi Dr. Greve,
I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI
task for our study.
There are 80 face-name pairs that we will use and the duration can be between
3.5 and 4.75 secs. I have used the following command:
sorry, I thought I answered this. those slight offsets are not
important, you can round to nearest TR
On 08/08/2017 10:57 PM, Ruthie Shaffer wrote:
> Hi all,
>
> I sent a message previously and just wanted to check in one more time
> about this question (apologies for the repeat message!).
>
>
Hi all,
I sent a message previously and just wanted to check in one more time about
this question (apologies for the repeat message!).
I’m using Optseq2 to generate stimulus / jitter schedules and, depending on the
TR I use, in the output files I see onset times like 124.4001 (instead of
those are not concerning, you can just round to the nearest TR
On 8/4/17 12:32 PM, Ruthie Shaffer wrote:
Hi,
I’m using Optseq2 to generate stimulus / jitter schedules, and,
depending on the TR used, in the output timing files I see several
event onset times very close to the correct time,
Hi,
I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on
the TR used, in the output timing files I see several event onset times very
close to the correct time, but slightly off (for example, something like
124.7999, instead of 124.8). I’ve used the following command
what is going wrong?
On 05/22/2017 12:11 PM, Tabassi Mofrad, F. wrote:
> Hi,
>
> I have a question about software input.
>
> --ntp 340 --tr 1.8 --psdwin 0 20 1.8 --ev L1 1.6 60 --ev L2 1.6 60
> --ev Blank 1.6 15 --evc 1 -1 0 --nkeep 3 --o IAPS --tnullmin 2
> --tnullmax 5.6 --nsearch 1
>
>
Hi,
I have a question about software input.
--ntp 340 --tr 1.8 --psdwin 0 20 1.8 --ev L1 1.6 60 --ev L2 1.6 60 --ev Blank
1.6 15 --evc 1 -1 0 --nkeep 3 --o IAPS --tnullmin 2 --tnullmax 5.6 --nsearch
1
Here is the input that I have provided but it is problematic. Please could you
let me
Hi Ruth, there are no ways to constrain the order of the stimuli in this
way in optseq. If the timing is fixed between these 3 items, then they
are effectively one stimulus type, and you can optimize the order of
that one stimulus type.
On 11/10/2016 01:31 PM, Ruthie Shaffer wrote:
> Hi all,
Hi all,
I’m posting to ask for advice on setting up certain parameters in optseq2:
Specifically, in optseq2, how can one set up parameters to best optimize a task
where there are say 20 items presented 3 times, where the relevant contrasts
are between the first, second, and third presentations
hello
i am trying to use optseq2 to design a study. I have a new mac book pro
with El Capitan installed. I have tried downloading all different optseq2
versions but each time when i try to run it through the terminal i get the
same exact error:
-bash: optseq2: command not found
what am i doing
Dear all,
I would like to download optseq2 from
https://surfer.nmr.mgh.harvard.edu/optseq/ it remains unavailable for
several days.
Is there any other way to obtain it ?
Regards,
Alexandre Obert
--
Alexandre OBERT
Doctorant en Psychologie Cognitive
Université de Reims Champagne-Ardenne
Thank you. Much appreciated.
Cheers,
PB
On Wed, Apr 22, 2015 at 6:25 PM Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
yes, it is available with the FreeSurfer source code, which you can
download
doug
On 04/22/2015 04:30 PM, Patrick Beukema wrote:
Hi,
Is it possible to get the source
On 04/21/2015 03:26 PM, Dan Goldman wrote:
Thanks for this. I should be more clear. The reasoning and figures
tasks are completely separate and are not being compared to each
other. Each task has two conditions. For example, in the reasoning
task, I have two conditions: Spatial and
yes, it is available with the FreeSurfer source code, which you can download
doug
On 04/22/2015 04:30 PM, Patrick Beukema wrote:
Hi,
Is it possible to get the source for optseq2. I would like to
translate it into python to integrate it into my existing scripts, and
also modify the output
Hi,
Is it possible to get the source for optseq2. I would like to translate it
into python to integrate it into my existing scripts, and also modify the
output files to include csv output options, instead of writing post hoc
scripts to change the output.
Thank you,
Patrick
Hello,
I have a question re: calculations of efficiency and vrf in optseq2.
We are running two tasks. One is a reasoning tasks, with trial lengths of
12 seconds. The other is an embedded figures task with trial lengths of 10
seconds. For both tasks, we have set a minimum ISI of 4 seconds and a
On 4/20/15 5:45 PM, Dan Goldman wrote:
Hello,
I have a question re: calculations of efficiency and vrf in optseq2.
We are running two tasks. One is a reasoning tasks, with trial lengths
of 12 seconds. The other is an embedded figures task with trial
lengths of 10 seconds. For both tasks, we
Hi Douglas,
Thank you for the quick response.
Could you tell me which version of optseq this is? Are there multiple
versions of optseq2?
On Mon, Apr 20, 2015 at 1:31 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
Can you try using this version of optseq?
I am having some trouble using this version- when I try to use it in
Terminal, it returns Permission denied. Is there something I need to do
to be able to use it on my computer?
Thanks for your help.
On Mon, Apr 20, 2015 at 1:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
This is the
Can you try using this version of optseq?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2
I changed some things that might fix this problem. I ran the command
line below with it, and it gave reasonable results for the last null.
On 4/20/15 1:22 PM, Dan Goldman wrote:
This is the most recent version, the one that will be part of FS version 6.
On 4/20/15 1:40 PM, Dan Goldman wrote:
Hi Douglas,
Thank you for the quick response.
Could you tell me which version of optseq this is? Are there multiple
versions of optseq2?
On Mon, Apr 20, 2015 at 1:31 PM,
Hello,
I am having a problem with optseq2, where the final NULL event is given a
much longer duration than the rest of the events. This happens even if I
set tnullmax to a lower number- for example, I set tnullmax to 10 seconds,
and the final interval came out at 48 seconds. Do you know how to
It seems that I am unable to run the file that you sent on a mac- is it a
different version from the one available for MacOSX here?
https://surfer.nmr.mgh.harvard.edu/optseq/
On Mon, Apr 20, 2015 at 2:53 PM, Dan Goldman dreindo...@gmail.com wrote:
Nevermind, I got it to work! Thanks for your
chmod a+x optseq2
On 4/20/15 2:13 PM, Dan Goldman wrote:
I am having some trouble using this version- when I try to use it in
Terminal, it returns Permission denied. Is there something I need to
do to be able to use it on my computer?
Thanks for your help.
On Mon, Apr 20, 2015 at 1:50 PM,
When I try that I get the error cannot execute binary file.
On Mon, Apr 20, 2015 at 2:46 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
chmod a+x optseq2
On 4/20/15 2:13 PM, Dan Goldman wrote:
I am having some trouble using this version- when I try to use it in
Terminal, it returns
Hi, I am trying to set up a design using optseq2, but the tnullmax command
doesn't seem to be functioning. the script runs and outputs files, but they
exceed the tnullmax which i specify. is anyone familiar with this issue?
this is what i am inputting:
--tr 2 --psdwin 0 20 1 --ev easy 4 36 --ev
This may be a bug that I fixed. Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2
On 02/06/2014 02:11 PM, Wei-chun Wang wrote:
Hi, I am trying to set up a design using optseq2, but the tnullmax
command doesn't seem to be functioning. the script runs and
Hi all,
I figured I would have some luck tapping expertise on using optseq2 in
this mailing list. There are 8 trials times 8 conditions in an
event-related design. We are using a 1-back task just to keep
participants paying attention. Thus, we are not attempting to match the
number of
Hi John, you would make the event last long enough to encompass all the
subevents. It might be a problem for optseq if you need to cue the
subject as to when to perform each subevent.
doug
On 9/12/13 6:23 PM, John Ryan wrote:
Hi all - I'm trying to design my first event related experiment,
Hi all - I'm trying to design my first event related experiment, and I'm
having trouble figuring out how to best optimize the design...wondering if
you have any insights:
I have two conditions (milkshake and water).
Each condition has several events in order: Participants get a squirt of
Dear optseq2 developers,
I would like to use optseq2 to develop optimal sequence for my MRI experiment.
I have a windows machine (Windows 7, SP1, 64-bit OS) so I installed Cygwin-64
to run the optseq2. What I've done so far:
- Downloaded optseq2.exe (Cygwin version) and put this into
...@nmr.mgh.harvard.edu] På vegne av Lukito, Steve
Sendt: 12. august 2013 12:31
Til: freesurfer@nmr.mgh.harvard.edu
Emne: [Freesurfer] Optseq2 with Cygwin
Dear optseq2 developers,
I would like to use optseq2 to develop optimal sequence for my MRI experiment.
I have a windows machine (Windows 7, SP1, 64
hello,
i'm struggling with how to specify a schedule and then ask optseq2 to identify
an optimal timing schedule. specifically i have a conditioned cue and an
unconditioned stimulus. the high threat CS always needs to follow with a high
pain US and low threat CS with a low pain CS. how can i
Hi Claire, you can't do this type of design in optseq because optseq
requires that there be no constraints of which stimulus can follow
itself or another stimulus (obviously this does not work for your
design). If you take a CS-US pair as a stimulus, then that should work.
Also, you could
Hello all,
A question regarding the usage of Optseq2
I have this command line
optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev ev40 2.5
20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o
OptSeq_TRIALS/3_null9_6 --nsearch 1
Now the efficiency tha I get is around
On 6/13/13 9:45 AM, A a wrote:
Hello all,
A question regarding the usage of Optseq2
I have this command line
optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev
ev40 2.5 20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o
OptSeq_TRIALS/3_null9_6 --nsearch 1
Dear FS-experts,
I've been using optseq for many years without problems, however, I run into a
couple now.
My code is the following:
optseq2 --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1 --ev Gain2 5.0
8.0 --ev Gain4 5.0 8.0 --ev Gain6 5.0 8.0 --ev Gain8 5.0 8.0 --ev Loss2 5.0 8.0
I think you are at the limit of what is possible. You have TR=2 and
Ntp=255 for a total scan time of 510sec. You have 9 event types, each
5stim+2null=7sec long, each repeated 8 times. This calls for 504 for
stimulation and so only 6 sec total left for jitter.
doug
On 05/13/2013 05:28 AM,
(1) Version: optseq2.c,v 2.21.2.1
(2) Computer operating system: Mac OS X Version 10.7.3
(3) Command line: Not relavant here
(4) Description of the problem: A trial in my experiment involves a
countdown (duration 2 seconds) followed by the event of interest (0.5
seconds) followed by a blank
In this case, the event will be 7 sec. The way it is set up, it assumes
that you will use an FIR model to analyze the results (ie, not assuming
a shape to the HRF), making it difficult to separate the various
subevents to the event (though you can assume a shape to the HRF). It is
appropriate
Dear list,
I have an optseq2 question, and would very much appreciate your time.
I'm having difficulty calculating the required number of timepoints. I'd like
to use --tnullmin and --tnullmax so as to have a null event in between each
trial, with a duration of 4-8 sec. I have 16 conditions, 6
Hi Hanah, I just found and fixed the bug. It was making the effective
tNullMax = tNullMin + your specified tNullMax. I've put a new (linux)
version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux
doug
On 05/09/2012 06:09 PM, Chapman, Hanah wrote:
Dear list,
Hi everyone, I'm using optseq2 and a tnullmin of 2 seconds to force 2 seconds
between each event for my paradigm, but I get a segmentation fault error.
Here's my command line below. I didn't specify a tnullmax, so that I would
avoid any errors by specifying both. I tried other values for
Hi Anita, you need to check the math on your design. You have 86
stimuli. Each stimulus requires 0.5s for presentation and 2 sec for null
means 215sec total (minimum). But you have TR=2 and Ntp=86 meaning a run
of only 172 sec. You will need to increase the number of TRs or
decrease the
Hi,
I was wondering if it is possible to use optseq2 to get null events (e.g.
fixation) between each event type. I would like to see the optimal sequence of
trials for a design that involves two event types (each 0.5 sec), 60 TRs for
one event, 26 TRs for the other, and a 2sec TR. I would like
Hi Doug and all,
In the output summary of optseq2, does the absolute value of the efficiency of
nominal ideal XtX matter when evaluating your design? Specifically, I'm
experimenting with different TR durations, and it looks like shorter TRs give
me lower efficiency values, but these values are
Hi there,
I noticed that when I include additional polynomials as nuisance variables, the
efficiency of the design decreases. When should we include polynomials to
account for scanner drift, and how do we decide the maximum order of the
polynomials? Does it depend only on the length of the
I usually use quadratic. I would not worry too much about trying to
extract out every last drop of efficiency. Things are going to change
enough when you actually analyze the data. What you want to do is just
avoid having really bad sequences.
doug
Leo Fernandino wrote:
Hi there,
I
Hi,
I am still curious whether and how the above mentioned feature could be
implemented into optseq2.
I would be delighted and very greatful to hear your ideas.
Cheers,
Tilman
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear Doug,
The command is still not known.
I think that our linux platform is too old...
Just to be sure :
- optseq2 need matlab ?
- optseq2 can be run even if Freesurfer and FS-FAST are not installed ?
thank you.
other wise, do you know another program doing similar things than
optseq ?
into the
sequence (optimized by optseq2). :)
Tilman
Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 2. März 2010 19:04
An: Gaber, Tilman
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential
...@nmr.mgh.harvard.edu]
Gesendet: Montag, 1. März 2010 19:08
An: Gaber, Tilman
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a
factor
Optseq2 does not have the ability to change the identity of the stimuli
during the run.
doug
Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as
a factor
Optseq2 does not have the ability to change the identity of the stimuli
during the run.
doug
Gaber, Tilman wrote:
Thank you for your quick response. Initially I had the same idea.
Unfortunately
@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as
a factor
You can specify that there are 4 trial types (AA, AB, BA, BB), and give
the duration twice that of the individual.
doug
Gaber, Tilman wrote:
Dear mailinglist recipients,
I am currently
Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Gesendet: Freitag, 26. Februar 2010 18:56
An: Gaber, Tilman
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a
factor
You can specify that there are 4 trial
Dear mailinglist recipients,
I am currently planning an optimized experiment using optseq2 and a 2x2 factors
behavioral response task (Simon-task).
The task consists of a pseudo-randomized series of two kinds of trials
(congruent and incongruent).
In addition there is a sequential factor,
You can specify that there are 4 trial types (AA, AB, BA, BB), and give
the duration twice that of the individual.
doug
Gaber, Tilman wrote:
Dear mailinglist recipients,
I am currently planning an optimized experiment using optseq2 and a 2x2
factors behavioral response task (Simon-task).
Hi Doug,
I reduced the total time points, however, I found the eff and VRF value all
became smaller as the time points decreased, and I still got some null
events more than 7s. If I set the time points as 470s, I got most 5-7 null
events, except the last 35s null event, and then its eff is 0.007,
Hi Doug,
I figure out why this happened and how to solve the problem. Because My
trials always lasted for 12,13,14s, and optseq2 believed that the baseline
should last about 12-14s, which means null time should be as many as one
task condition or the average of the task conditions. I set my
I think your constraint of 5-7 null time is too tight for optseq, and
you may still have too much time in your run to make 5-7 work. It's hard
to say whether the VRFAvg is good enough or not. You are using sub-TR
estimation during the optimization. If you are going to assume a shape
to the
I think this is partially a bug in optseq and partially a problem with
your design. You have a total amount of stimulation time =
12*9+13*8+14*8+12*9+13*8+14*8 = 648 sec. Your run lasts 500*2 = 1000
sec, so the total amount of fixation time is 1000-648 = 352 sec. You
have 8*4+9*2 = 50 stimuli,
By using tr=2, delta psd = 2 (ie, --pwdwin 0 20 2), and tnullmax=2, you
are forcing each null to be exactly 0 or 2 sec, and optseq is having a
hard time with such a hard constraint. You can try changing delta psd to 1.
doug
Kathrin Herbst wrote:
Hi,
I am having a related problem:
I don't
jitter the
ISI than? manually?
3. thanks.
*From:* Doug Greve gr...@nmr.mgh.harvard.edu
*To:* Asaf Kaftory asaf_kaft...@yahoo.com
*Cc:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Saturday, September 26, 2009 7:42:43 PM
*Subject:* Re: [Freesurfer] optseq2 help: DPSD and jitter
On Sat, 26 Sep
.
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Asaf Kaftory asaf_kaft...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tue, October 6, 2009 6:16:37 PM
Subject: Re: [Freesurfer] optseq2 help: DPSD and jitter
I don't know what two samples refers to.
doug
Asaf Kaftory wrote
is clearer now,
Asaf.
*From:* Douglas N Greve gr...@nmr.mgh.harvard.edu
*To:* Asaf Kaftory asaf_kaft...@yahoo.com
*Cc:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Tue, October 6, 2009 6:16:37 PM
*Subject:* Re: [Freesurfer] optseq2
.
From: Doug Greve gr...@nmr.mgh.harvard.edu
To: Asaf Kaftory asaf_kaft...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Saturday, September 26, 2009 7:42:43 PM
Subject: Re: [Freesurfer] optseq2 help: DPSD and jitter
On Sat, 26 Sep 2009, Asaf Kaftory wrote:
Hello list,
I'm new
.
From: Doug Greve gr...@nmr.mgh.harvard.edu
To: Asaf Kaftory asaf_kaft...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Saturday, September 26, 2009 7:42:43 PM
Subject: Re: [Freesurfer] optseq2 help: DPSD and jitter
On Sat, 26 Sep 2009, Asaf Kaftory wrote:
Hello list,
I'm new
Hello list,
I'm new to optseq, and would like your help with the following issues:
1. What exactly does DPSD mean? and why does the TR has to be an integer of it?
2. My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i
On Sat, 26 Sep 2009, Asaf Kaftory wrote:
Hello list,
I'm new to optseq, and would like your help with the following issues:
1. What exactly does DPSD mean? and why does the TR has to be an integer of
it?
Delta Post-Stimulus Delay. The time between samples in the
FIR. Usually, it is just
Hi,
I am trying to design an event-related memory encoding task. Simply
put, the subject either sees familiar or novel pictures (the familiar
ones having been shown outside of the scanner before hand). After
scanning, recognition for the pictures is tested. I am interested in
the novel
Aaron Trachtenberg wrote:
Hi,
I am trying to design an event-related memory encoding task. Simply
put, the subject either sees familiar or novel pictures (the familiar
ones having been shown outside of the scanner before hand). After
scanning, recognition for the pictures is tested. I am
Hongchuan Zhang wrote:
Hi, list,
I am new to optseq2 so I really need advices to my questions. We have
an experiment of 2 factors with36 trials for each factor, and another
24 null trials. So in total we have 96 trials. We also have 3 random
jitters which make our trials could last for
Hi, list,
I am new to optseq2 so I really need advices to my questions. We have an
experiment of 2 factors with 36 trials for each factor, and another 24 null
trials. So in total we have 96 trials. We also have 3 random jitters which make
our trials could last for either 4.6, 5 or 5.4
Hello
I am running optseq2 on Mac OS X, v.10.5.4. Over the past 2 days, Optseq2 has
been crashing after running for a few minutes. It will run along smoothly, and
then suddenly:
optseq2(22653) malloc: *** error for object 0x3be83b0: incorrect checksum for
freed object - object was probably
Hello all,
I am new to Optseq2 and I have a question about generating 2-way design
orders using the program and about a question about temporal jitter. I am
working on a design with 7 conditions. I have run the following design
through optseq2 and gotten out reasonable looking orders.
--ntp
BumSeok,
You'll want to use the centos5_x64_64 freesurfer installation. I'm
guessing you're using the rh9 freesurfer installation (see the build-
stamp.txt file in the freesurfer dir to confirm), as libstdc++.so.5 is
used in that distribution.
Or, if you got optseq from the optseq2 webpage,
It looks like you have an awful lot of null in there
(6+7+8+6+7+8+11)*2 = 106 sec of stimulation
The total run length is 130*2 = 260 sec
Leaving 260-106 = 154 sec for null.
There are only 7*2=14 events total,
so the average null will be 154/14 = 11 sec
I'm surprised that one null was 75 sec,
Dear List -
I have a question about how long I should expect it takes my computer to
generate optseq2 sequences. A colleague advised that I should expect it
to take a couple hours to generate sequences. I've just produced 20
sequences (nsearch = 1; see below for full command line specs)
If it searched 10,000 iterations, that's probably fine. If it only takes
a few min to do 10k, I might let it run over 100k, though it probably
won't improve much.
doug
Shannon Tubridy wrote:
Dear List -
I have a question about how long I should expect it takes my computer
to
Hi,
Optseq2 is returning designs where the last NULL
even is upwards of 75 seconds (more than 4 times my
psdMax!. Can I keep the rest of the order as is, and
just truncate the last NULL event to be equal to my
PsdMax value? Below is my command and a sample output
file:
optseq2 --ntp 130 --tr 2
Hi, I have a question concerning optseq2.
I found that increasing the dPSD Parameter from 1/2 TR (0.92s) to 1 TR
(1.84s) INCREASED the efficiency of the best schedules from about .075 to
.093.
I would have assumed that a more finely spaced schedule would result in
better efficiency scores. Did I
Hello,
I am trying to run optseq2 but i am getting an error message.
Here is the command I use:
optseq2 --ntp 160 --ev AL 4 16 --ev AR 4 16 --ev PL 4 16 --ev PR 4 16
--o AS --nkeep 12 --log ASfMRI --nsearch 1 --psdwin 2 20 --tnullmin 2
--tnullmax 8 --tr 2 --sum ASfMRI-sum
here is the
I'm new to optseq and to rapid E-R designs generally. I have a two
questions about it. If it helps, here's my (tentative) design - I'm
creating a task with 5 conditions (including rest) with a TR of 2320 ms
and trial SOA of 4640 ms (my stimuli are on screen for 1 sec of this time).
1) I've
John Herrington wrote:
I'm new to optseq and to rapid E-R designs generally. I have a two
questions about it. If it helps, here's my (tentative) design - I'm
creating a task with 5 conditions (including rest) with a TR of 2320 ms
and trial SOA of 4640 ms (my stimuli are on screen for 1 sec
Susan Mosher wrote:
Greetings Freesurfers,
I am using optseq2 for the first time to generate a stimulus order for my
trials and figure out the ideal ITI between trials. I have a few
questions
about how this works.
1. I tried specifying the PSD max as 18 seconds and minimum of 2
seconds.
Greetings Freesurfers,
I am using optseq2 for the first time to generate a stimulus order for my
trials and figure out the ideal ITI between trials. I have a few questions
about how this works.
1. I tried specifying the PSD max as 18 seconds and minimum of 2 seconds.
My ntp is 216 and my TR is
what do you mean by allowable null intervals? If you mean that there
needs to be a fixed amount of time between two stimuli, then you cannot
use optseq for this. However, you can tell optseq that there are only
two stimuli, which each stimulus is a pair. Then you'd have to go back
and recode
Thanks a lot for your message. It definitely helped me because I really need
optseq but I am not very confident with it.
If I understand correctly, for 10 stim of 1.5 sec and a protocol with a TR of
4s, a correct optseq sequence would be like that:
--ntp 15 --tr 4 --psdwin 0 18 1.5 (or 0.5) --ev
Hello list,
I am new to optseq2 and I would need some help with it.
I have a very long experiment (many stimuli) and on top of that I have a long TR
(4s) because I collect 60 coronal slices covering all the brain.
My stimuli are quite short 1.5s or 2.5s but according to optseq the stimuli
Hi Giorgio,
There are some refs at the end of the --help.
doug
On Sat, 22 Apr 2006, Giorgio Ganis wrote:
Hi,
What would be the most appropriate paper/TechRep to cite for optseq2
credits? Thanks.
-Giorgio
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Hi,
What would be the most appropriate paper/TechRep to cite for optseq2
credits? Thanks.
-Giorgio
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I have a question regarding programming fMRI experiments. I am programming a
source memory experiment and would like to do ROC modeling with the data.
Therefore, I would need to record two responses from participants in each test
trial (i.e., Red, Blue, New; and 1, 2, 3). I am wondering if
Hi Christie,
I can't comment on whether getting the two responses is the right way
to go, but it sounds like you've run optseq properly.
doug
On Wed, 19 Oct 2005, Christie Chung wrote:
Hi,
I have a question regarding programming fMRI experiments. I am programming a
source memory
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