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 different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects.
My design will have two columns : main effect of moving hand and the 1 order.
My contrast will be like this [1 0; 0 1]
This is what I would like to optimize using OptSeq2:
Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds
I am not sure whether I should use null events or the Period between movement is enough.
Also my main aim is to optimize the best design in terms of detection.
Please any guide or help
Thanks
AS
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 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 different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects.
My design will have two columns : main effect of moving hand and the 1 order.
My contrast will be like this [1 0; 0 1]
This is what I would like to optimize using OptSeq2:
Event design
- ISI 6 seconds + or - 1.5 seconds ( I could not do this
- TR 3
- volumes 150
- 45 hand movement; 15 at each target level ( I could not do this )
- each movement lasts for 3 seconds
I am not sure whether I should use null events or the Period between movement is enough.
Also my main aim is to optimize the best design in terms of detection.
Please any guide or help
Thanks
AS
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Prof Douglas,
Thanks for your response.
I managed to do the following:
optseq2 --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45 --nkeep 3 --o trial --nsearch 10000
Now what I really want to do is to make the ISI 7 seconds + or - 1.5 seconds. I am not sure how I should use the percentage option if this is what I should change plus the ISI time?
I hope this clarifies it more
Regards,
AS
On 10 Jun 2013, at 16:21, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 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 different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects.
My design will have two columns : main effect of moving hand and the 1 order.
My contrast will be like this [1 0; 0 1]
This is what I would like to optimize using OptSeq2:
Event design
- ISI 6 seconds + or - 1.5 seconds ( I could not do this
- TR 3
- volumes 150
- 45 hand movement; 15 at each target level ( I could not do this )
- each movement lasts for 3 seconds
I am not sure whether I should use null events or the Period between movement is enough.
Also my main aim is to optimize the best design in terms of detection.
Please any guide or help
Thanks
AS
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
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 10000
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 - 1.5 seconds.
Any help please ?
Another point is about the psdwin, I am not sure what exactly it represents. I saw your slides but I thought this should also change the ISI,. Can you comment on it please ?
Thanks
AS
On Mon, Jun 10, 2013 at 5:49 PM, fMRI fmri2013@gmail.com wrote:
Dear Prof Douglas,
Thanks for your response.
I managed to do the following:
optseq2 --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45 --nkeep 3 --o trial --nsearch 10000
Now what I really want to do is to make the ISI 7 seconds + or - 1.5 seconds. I am not sure how I should use the percentage option if this is what I should change plus the ISI time?
I hope this clarifies it more
Regards,
AS
On 10 Jun 2013, at 16:21, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 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 different target level ( say 10 20 30). Then I
will model them as a one condition and enter the parametric response as a first order polynomial effects.
My design will have two columns : main effect of moving hand and the 1
order.
My contrast will be like this [1 0; 0 1]
This is what I would like to optimize using OptSeq2:
Event design
- ISI 6 seconds + or - 1.5 seconds ( I could not do this
- TR 3
- volumes 150
- 45 hand movement; 15 at each target level ( I could not do this )
- each movement lasts for 3 seconds
I am not sure whether I should use null events or the Period between
movement is enough.
Also my main aim is to optimize the best design in terms of detection.
Please any guide or help
Thanks
AS
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . 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.
The PSD Window is the time over which you expect the hemodynamic response to last. If your event lasts 3 sec, I would put 21, so "--psdwin 0 21 3". If you want to constraint the ISI to be between 5.5 and 8.5 sec, then use "--tnullmin 5.5 --tnullmax 8.5"
Also, you need at least 3*20*(3+7) = 600sec = 200 time points of scanning time
doug
On 06/10/2013 01:47 PM, A a wrote:
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 10000
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 - 1.5 seconds.
Any help please ?
Another point is about the psdwin, I am not sure what exactly it represents. I saw your slides but I thought this should also change the ISI,. Can you comment on it please ?
Thanks
AS
On Mon, Jun 10, 2013 at 5:49 PM, fMRI <fmri2013@gmail.com mailto:fmri2013@gmail.com> wrote:
Dear Prof Douglas, Thanks for your response. I managed to do the following: optseq2 --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45 --nkeep 3 --o trial --nsearch 10000 Now what I really want to do is to make the ISI 7 seconds + or - 1.5 seconds. I am not sure how I should use the percentage option if this is what I should change plus the ISI time? I hope this clarifies it more Regards, AS On 10 Jun 2013, at 16:21, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > 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 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 different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. >> >> My design will have two columns : main effect of moving hand and the 1 order. >> >> My contrast will be like this [1 0; 0 1] >> >> This is what I would like to optimize using OptSeq2: >> >> Event design >> 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this >> 2) TR 3 >> 3) volumes 150 >> 4) 45 hand movement; 15 at each target level ( I could not do this ) >> 5) each movement lasts for 3 seconds >> >> I am not sure whether I should use null events or the Period between movement is enough. >> >> Also my main aim is to optimize the best design in terms of detection. >> >> Please any guide or help >> >> Thanks >> >> >> AS >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > http://www.partners.org/complianceline . 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@nmr.mgh.harvard.edu
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A a -
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fMRI