External Email - Use Caution
Hi,
We are attempting to use optseq2 for a study design where the events last 5
seconds. ?
I've found previous answers that indicate that PSDWIN max should be set between
21 to 24 seconds if your event is 3 seconds in length.
For 5 seconds in leng
on behalf of Douglas N Greve
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
n behalf of Douglas N Greve
>
> *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:
> &
on behalf of Douglas N Greve
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 qu
t; *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 sc
on behalf of Douglas N Greve
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
bccl/
> Phone:_ (305)284-3286_
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N Greve
>
> *Sent:* Wednesday, December 20, 2017 6:38:48 PM
> *To:* freesurfer@nmr.mgh.harv
> *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/?u
...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
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:/
psy.miami.edu/bccl/
> Phone:_ (305)284-3286_
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N Greve
>
> *Sent:* Wednesday, December 20, 2017 3:40:48 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Optseq Help
> C
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
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
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-condti
Department of Psychology
University of Miami
Website: http://www.psy.miami.edu/bccl/
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
/bccl/
Phone: (305)284-3286
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
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
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
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 ou
tha is
>
> Aser
>
>
> Sent from my Samsung Galaxy smartphone.
>
> Original message
> From: fmri2013
> Date: 10/11/2017 19:30 (GMT+00:00)
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs
>
using a specific software.
Many tha is
Aser
Sent from my Samsung Galaxy smartphone.
Original message From: fmri2013 Date:
10/11/2017 19:30 (GMT+00:00) To: Freesurfer support list
Subject: Re: [Freesurfer] Optseq and de
convolution for rapid designs
Many thanks Douglas
If
Sorry, those kinds of constraints, ie, requiring some events to be in a
certain order, are not possible in optseq.
On 11/15/2017 08:44 PM, Michelle VanTieghem wrote:
> Hello,
>
> I am using optseq to optimize a new task. I have been playing around
> with the examples they have on the documentat
Hello,
I am using optseq to optimize a new task. I have been playing around with
the examples they have on the documentation. What I can't find is
information on how to set up the trial structure when 1 trial is comprised
of 3 different stimuli types:
(choice 3sec --> effort (hard or easy) 3 sec -
Galaxy smartphone.
Original message From: Douglas Greve
Date: 10/11/2017 19:24 (GMT+00:00) To:
freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de
convolution for rapid designs
It is because the random jitter creates differential amounts of
overlap
It is because the random jitter creates differential amounts of overlap.
Imagine if you have A=C+D and B=C-D. You know A and B, but you want C
and D. You have two equations and two unknowns, so you can solve for C
and D from A and B eventhough C and D "overlap" in A and B and you never
see C or
Hi all
I used Optseq to optimize rapid event designs with multiple conditions . I
have a theortical question : how it is possible to distingwoh the close by
trials ? Is it by de convoution ? How is it possible to deal with
overallped trials ?
Is it because the conditions are random so that when
Yea, 26 sec should be ok
On 12/07/2016 02:46 PM, Xavier Guell Paradis wrote:
> Dear FS team,
> I have one short question regarding Optseq:
> What is the recommended psdwinMAX value for events of 8s?
> I have read in this forum that events of 3s should have a psdwinMAX of
> 21s or even 24s; does
Dear FS team,
I have one short question regarding Optseq:
What is the recommended psdwinMAX value for events of 8s?
I have read in this forum that events of 3s should have a psdwinMAX of 21s or
even 24s; does this mean that events of 8s should have a psdwinMAX of 26-29s?
Thank you very much,
Xavi
The command line looks ok. The low efficiency is coming from the low
number of events per event type.
On 9/27/16 9:52 AM, Alexandre Obert wrote:
Dear all,
I would like to optimize my design by inserting null-events between my
trials (in order to better catch the HRF shape with reasonable
du
Dear all,
I would like to optimize my design by inserting null-events between my
trials (in order to better catch the HRF shape with reasonable duration of
the experiment) using optseq.
I'm not very familiar with this useful tool and I wonder if you could check
my setup?
Here my design :
I've got
Hi Goi, please remember to post to the freesurfer list. Thanks! The max
psd depends upon how long it takes for the HRF to return to baseline
(and do not related to the TR). This is usually something like 20 sec +
the duration of your stimulus.
doug
On 2/17/14 1:31 PM, Goi Khia Eng wrote:
No, sorry. You might be able to treat two consecutive trials as a single
trial, but then you won't get jitter between them.
doug
On 12/10/2013 02:38 PM, Chris McNorgan wrote:
> Hi all,
>
> I posed a question back in November but got no replies, so I'll try to
> restate it briefly:
>
> Is there
Hi all,
I posed a question back in November but got no replies, so I'll try to
restate it briefly:
Is there a means of enforcing at least one set of consecutive trials for
a condition in an optseq schedule (or even consecutive trials with an
intervening NULL event)?
I am trying to produce a s
you might need to reduce the number of TRs
On 6/20/13 10:34 AM, A a wrote:
Hi all,
Is there a rule that let me avoid having the error message could not
force null max?
-- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3
15 --ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4
Hi all,
Is there a rule that let me avoid having the error message could not force
null max?
-- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3 15
--ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4.5 ..
Thanks
AS
___
Freesurfer maili
I would not agonize about getting the maximum possible efficiency. When
you go to analyze your data, there will be differences that you cannot
control (eg, including motion correction regressors or temporal
whitening), and these will change efficiency. The only thing I would
change to the comm
Dear Prof Douglas,
I asked this before but I would like to understand what I am doing and also
need your recommendation.
I have three conditions : squeezes at three different levels. My aim is that I
want to use spm to enter them as a one condition and then enter the parametric
response as a c
Hi Ella,
On 6/16/13 9:27 AM, Ella Hinton wrote:
Hi all,
I have been advised to use optseq to aid my event related fMRI design,
specifically to help calculate stimulus order and timing. I've read
the help in some detail but am still a little unclear on some of the
appropriate values to input
Hi all,
I have been advised to use optseq to aid my event related fMRI design,
specifically to help calculate stimulus order and timing. I've read the help in
some detail but am still a little unclear on some of the appropriate values to
input and indeed what values I am aiming for in the outp
Correction
This is the lats code :
optseq2 --ntp 140 --tr 3 --psdwin 6 15 3 --ev ev20 3 20 --ev ev40 3 20
--ev ev60 3 20 --nkeep 3 --o OptSeq_TRIALS/trial_squ --nsearch 1
So The duration is 3 seconds for each and each repeat it 20 times. What I
need is to change/add the ISI to be 7 + or - 1
Hi, can you at least come up with an optseq2 command line that I could
then help you with? There are lots of examples on the web page. You
should be able to get to a point where you have an error.
thanks
doug
On 06/10/2013 05:14 AM, fMRI wrote:
> Hello all,
>
> This is my first question in this
Hello all,
This is my first question in this list and it is about OptSeq2.
I am nee to this command.
In brief, I wish to insert the following but Some of them I could not handle it:
My experiment has three conditions although I will later specify them as one
condition:
Moving hand at three d
Hi Hanah, I found another bug with the way that tNullMin was being
implemented which causes this problem. You can get the new version from
here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux
doug
On 05/14/2012 08:47 AM, Hanah Chapman wrote:
> Dear Doug,
>
> Thank y
Hi,
I'm planning to run an auditory experiment using a pseudo-sparse sampling
design. Something like: 4 sec stim period + 2 sec acquisition + 4 sec stim
period + 2 sec acquisition ...
So for example, I'd like to find an optimal sequence for a design with a TR
of 6 seconds but where the stimulus
S >> <mailto:florence.borge...@univ-st-etienne.fr>>
>>> *Cc : *freesur...@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>> *Objet : **Rép : [Freesurfer] optseq installation*
>>>
>>> Did you make it executable? They are
rence POMARES a écrit :
Début du message réexpédié :
De : Douglas N Greve
Date : 12 mars 2010 20:09:57 HNEC
À : Florence POMARES
Cc : freesurfer@nmr.mgh.harvard.edu
Objet : Rép : [Freesurfer] optseq installation
Did you make it executable? They are run from the shell, not matlab.
doug
Flo
Did you make it executable? They are run from the shell, not matlab.
doug
Florence POMARES wrote:
> Dear Optseq Developpers,
>
> Few years ago we used to design our paradigm with optseq. We would
> like to use it again but we can't install it.
> We went on the web site : http://surfer.nmr.mgh.ha
Dear Optseq Developpers,
Few years ago we used to design our paradigm with optseq. We would
like to use it again but we can't install it.
We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/
we download the linux version 2
we upload it to the our old linux server with matlab
opt
I think I would just optimize with one condition and then do the
post-hoc sorting into 5. It should be ok if the subject is responding
randomly. I don't have a tool for power, but optseq will give the
variance reduction factor, which goes in the denominator of the t-test.
This assumes you are
Hello--
I'm designing an event-related task that does not have predefined
conditions. instead, I plan to do some post-hoc sorting based on
performance and stimuli characteristics. I expect that after sorting,
I will have 5 conditions- but it could be more or less. Is it
advisable to deter
You need to set up the psdwin to span the duration of a hemodynamic
response to your event as if it were presented in isolation. For a 3sec
event, you can probably use something like 24 sec (so min=0, max=24).
Since your TR=2, but your event duration is 3sec, I'd set dpsd=1 (so
that both the TR
Hi,
I have 2 questions.
1) How do I calculate psd min, max, and dpsd. Is there a formula for
calculating these values? I have 4 kinds of stimuli, stim duration = 3s,
stim repetition = 25, TR =2 so:
optseq2 --ntp 180 --tr 2 --psdwin [?] --ev A 3 25 --ev B 3 25 --ev C 3 25
--ev D 3 25 --o 4type
Have you tried using optseq2? Haven't used optseq in a long time:).
Mithra wrote:
Hello,
I am trying to use the optseq command for 2 conditions of 30 trials
each with TR = 2
optseq -ntp 120 -TR 2 -npercond 30 30 -tpercond 3 3 -nsessions 3
-label critical independent -o TestFile
I get the fol
Hello,
I am trying to use the optseq command for 2 conditions of 30 trials
each with TR = 2
optseq -ntp 120 -TR 2 -npercond 30 30 -tpercond 3 3 -nsessions 3
-label critical independent -o TestFile
I get the following result:
-0.0001 3.000 critical
4.0001 3.000 critical
Dear List:
I have a question concerning optimizing the presentation of a psycho-
metric SCASE procedure with optseq. Subjects will view two
interleaved SCASE in the scanner. SCASE1 and SCASE2 test the whole
length of stimuli strengths for two different conditions. To obtain
the best sequen
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