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 duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5 stim and a 2.5 artificial "null" event which is different than the null event optseq estimates).
I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead?
2 Also, would a psdwin of 20s be enough for a 4 sec stimulus?
3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run longer.
4 Is the previous version of optseq still available? I only found optseq2 on your website. Thanks a lot for your help. Tamara
The stim duration does not have to be a multiple of the TR. If has to be a mult of the dPSD, which you can set to 0.5sec.
Tamara Cristescu wrote:
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 duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5 stim and a 2.5 artificial "null" event which is different than the null event optseq estimates).
I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead?
You have to set psdwin.
2 Also, would a psdwin of 20s be enough for a 4 sec stimulus?
I'd probably go to 24.
3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run longer.
It should not, though the last stimulus may extend behyond the last time point.
4 Is the previous version of optseq still available? I only found optseq2 on your website.
It should still be in the freesurfer distribution.
Thanks a lot for your help. Tamara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 ev1 1.5 10 -- etc..
dPSD or samplng interval should be a multiple of stimulus and PSDmin and max are set to correspond to haemodynamic response function (in this case I just multiplied the length of the stimulus by 12 to give enough time to accommodate the stim). Thanks you again for your help. Yours, Tamara
In message 462E641C.2000508@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu writes:
The stim duration does not have to be a multiple of the TR. If has to be a mult of the dPSD, which you can set to 0.5sec.
Tamara Cristescu wrote:
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 duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5 stim and a 2.5 artificial "null" event which is different than the null event optseq estimates).
I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead?
You have to set psdwin.
2 Also, would a psdwin of 20s be enough for a 4 sec stimulus?
I'd probably go to 24.
3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run longer.
It should not, though the last stimulus may extend behyond the last time point.
4 Is the previous version of optseq still available? I only found optseq2 on your website.
It should still be in the freesurfer distribution.
Thanks a lot for your help. Tamara
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Almost, you'll have to use
--psdwin 0 18 0.5
dPSD should be a multiple divisor of your TR and your stimulus length. Does your fMRI run only last for 15 time points? That's not very long
doug
Tamara Cristescu wrote:
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 ev1 1.5 10 -- etc..
dPSD or samplng interval should be a multiple of stimulus and PSDmin and max are set to correspond to haemodynamic response function (in this case I just multiplied the length of the stimulus by 12 to give enough time to accommodate the stim). Thanks you again for your help. Yours, Tamara
In message 462E641C.2000508@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu writes:
The stim duration does not have to be a multiple of the TR. If has to be a mult of the dPSD, which you can set to 0.5sec.
Tamara Cristescu wrote:
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 duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5 stim and a 2.5 artificial "null" event which is different than the null event optseq estimates).
I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead?
You have to set psdwin.
2 Also, would a psdwin of 20s be enough for a 4 sec stimulus?
I'd probably go to 24.
3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run longer.
It should not, though the last stimulus may extend behyond the last time point.
4 Is the previous version of optseq still available? I only found optseq2 on your website.
It should still be in the freesurfer distribution.
Thanks a lot for your help. Tamara
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
No it's not only 150 time points. All the experiment lasts around 45-50min and is made of 12 independent (but similar) stimulation blocks. Each block contains an exposure and an evaluation block (separate) during which stimuli are presented in an event-related manner. In plan to separate all blocks with long rest intervals (around 12s or 3 TRs) but I want to use optseq to optimise stimuli presentation in each block. I calculated the ntp as nr of stim * duration. I didn't model the null events explicitely and maybe that's why the stimulation schedule estimated by optseq has more time points than I put into the estimation parameters. I saw you didn't model the null in your examples and your estimated schedule was also longer than the original ntp. Thank you again for your help.
Yours,
Tamara
In message 462F7926.6090709@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu writes:
Almost, you'll have to use
--psdwin 0 18 0.5
dPSD should be a multiple divisor of your TR and your stimulus length. Does your fMRI run only last for 15 time points? That's not very long
doug
Tamara Cristescu wrote:
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 ev1 1.5 10 -- etc..
dPSD or samplng interval should be a multiple of stimulus and PSDmin and max are set to correspond to haemodynamic response function (in this case I just multiplied the length of the stimulus by 12 to give enough time to accommodate the stim). Thanks you again for your help. Yours, Tamara
In message 462E641C.2000508@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu writes:
The stim duration does not have to be a multiple of the TR. If has to be a mult of the dPSD, which you can set to 0.5sec.
Tamara Cristescu wrote:
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 duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5
stim and
a 2.5 artificial "null" event which is different than the null event optseq estimates).
I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead?
You have to set psdwin.
2 Also, would a psdwin of 20s be enough for a 4 sec stimulus?
I'd probably go to 24.
3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run
longer.
It should not, though the last stimulus may extend behyond the last time point.
4 Is the previous version of optseq still available? I only found optseq2 on your website.
It should still be in the freesurfer distribution.
Thanks a lot for your help. Tamara
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center 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@nmr.mgh.harvard.edu
-
Doug Greve -
Tamara Cristescu