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 understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event? 3. Is it true that jitter in optseq is made by inserting "NULLS", and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
hope to hear from you soon, Asaf.
On Sat, 26 Sep 2009, Asaf Kaftory wrote:
Hello list,
I'm new to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
Hey Doug - first of all, thanks for the reply. second -
1. I'm afraid i didn't get the explanation. what is the FIR, and what does it mean "two samples in the FIR" ?
2. ok, thanks. isn't it strange though? how do researches jitter the ISI than? manually?
3. thanks.
________________________________ From: Doug Greve greve@nmr.mgh.harvard.edu To: Asaf Kaftory asaf_kaftory@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 to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
Hey Doug - first of all, thanks for the reply. second -
1. I'm afraid i didn't get the explanation. what is the FIR, and what does it mean "two samples in the FIR" ?
2. ok, thanks. isn't it strange though? how do researches jitter the ISI than? manually?
3. thanks.
________________________________ From: Doug Greve greve@nmr.mgh.harvard.edu To: Asaf Kaftory asaf_kaftory@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 to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
I don't know what "two samples" refers to.
doug
Asaf Kaftory wrote:
Hey Doug - first of all, thanks for the reply. second -
- I'm afraid i didn't get the explanation. what is the FIR, and what
does it mean "two samples in the FIR" ?
- ok, thanks. isn't it strange though? how do researches jitter the
ISI than? manually?
- thanks.
*From:* Doug Greve greve@nmr.mgh.harvard.edu *To:* Asaf Kaftory asaf_kaftory@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 to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello list,
attached is my first post plus my new questions underneath every paragraph. thanks.
I'm new to optseq, and would like your help with the following issues:
- What exactly does DPSD mean? and why does the TR has to be an
integer of it?
Doug: Delta Post-Stimulus Delay. The time between samples in the FIR. Usually, it is just the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
Asaf: I'm afraid i didn't get the explanation. what is the FIR, and what
are the the samples in it ?
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
Doug: That is right. Sorry, don't know of anything that will give you with-in event jitter.
Asaf: ok, thanks. isn't it strange though? how do researches jitter the
ISI than? manually?
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Doug: Yes.
Asaf: thanks.
hope all is clearer now, Asaf.
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Asaf Kaftory asaf_kaftory@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:
Hey Doug - first of all, thanks for the reply. second -
- I'm afraid i didn't get the explanation. what is the FIR, and what
does it mean "two samples in the FIR" ?
- ok, thanks. isn't it strange though? how do researches jitter the
ISI than? manually?
- thanks.
*From:* Doug Greve greve@nmr.mgh.harvard.edu *To:* Asaf Kaftory asaf_kaftory@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 to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
FIR stands for "Finite Impulse Response". You define a time window that brackets your stimulus response then compute the average response at each time point inside the window. Eg, the window might start at stimulus onset (psd=0) and be sampled at each TR (eg, 2 sec) until the end of the window (eg, 26 sec). You can then plot the average at each time to see what the response looks like. See the Dale and Buckner paper (1998?) for more details. The FIR makes the fewest assumptions about the shape of the hemodynamic response (the opposite extreme is assuming a gamma function or difference of gammas).
It is almost impossible to analyze the separate components inside of a compound event unless you assume a shape to the function. I don't know what people do who want to have randomization inside a compound event. Probably just use their computers "rand" function.
doug
Asaf Kaftory wrote:
Hello list,
attached is my first post plus my new questions underneath every paragraph. thanks.
I'm new to optseq, and would like your help with the following issues:
- What exactly does DPSD mean? and why does the TR has to be an
integer of it?
Doug: Delta Post-Stimulus Delay. The time between samples in the FIR. Usually, it is just the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
Asaf: I'm afraid i didn't get the explanation. what is the FIR, and what
are the the samples in it ?
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
Doug: That is right. Sorry, don't know of anything that will give you with-in event jitter.
Asaf: ok, thanks. isn't it strange though? how do researchesjitter the
ISI than? manually?
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Doug: Yes.
Asaf: thanks.hope all is clearer now, Asaf.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Asaf Kaftory asaf_kaftory@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:
Hey Doug - first of all, thanks for the reply. second -
- I'm afraid i didn't get the explanation. what is the FIR, and what
does it mean "two samples in the FIR" ?
- ok, thanks. isn't it strange though? how do researches jitter the
ISI than? manually?
- thanks.
*From:* Doug Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* Asaf Kaftory <asaf_kaftory@yahoo.com
mailto:asaf_kaftory@yahoo.com>
*Cc:* freesurfer@nmr.mgh.harvard.edu
mailto: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 to optseq, and would like your help with the following issues:
- 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 the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic "tick" of the clock.
- My experiment design uses jitter - both ITI (i.e., between
trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event?
That is right. Sorry, don't know of anything that will give you with-in event jitter.
- Is it true that jitter in optseq is made by inserting "NULLS",
and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right?
Yes.
doug
hope to hear from you soon, Asaf.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Asaf Kaftory -
Doug Greve -
Douglas N Greve