Hi Doug,
I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks.
We used to shift our raw data by 2 TRs when we were using SPM.
How can we do this in FreeSurfer?
Thank you,
Sarah
You can use the -delay flag in mkanalysis-sess
doug
On 03/28/2018 05:35 PM, Sarah Cole wrote:
Hi Doug,
I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks.
We used to shift our raw data by 2 TRs when we were using SPM.
How can we do this in FreeSurfer?
Thank you,
Sarah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug.
I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation.
Do you have any recommendations?
Thanks, Sarah
On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
You can use the -delay flag in mkanalysis-sess
doug
On 03/28/2018 05:35 PM, Sarah Cole wrote:
Hi Doug,
I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks.
We used to shift our raw data by 2 TRs when we were using SPM.
How can we do this in FreeSurfer?
Thank you,
Sarah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
not sure what you are trying to do. can you send a picture? the default lag is TR/2
On 3/29/18 2:30 PM, Sarah Cole wrote:
Thanks, Doug.
I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation.
Do you have any recommendations?
Thanks, Sarah
On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
You can use the -delay flag in mkanalysis-sess doug On 03/28/2018 05:35 PM, Sarah Cole wrote: > Hi Doug, > > I have a block design experiment. After analyzing the data and > plotting the response magnitude across the TRs, we see that there is a > systematic lag in the response. For example, in a 16s block (TR=2s), > at TR-1 and TR-2 the response goes down and then starts rising from > TR-3. This is consistent across the subjects and blocks. > > We used to shift our raw data by 2 TRs when we were using SPM. > > How can we do this in FreeSurfer? > > Thank you, > > Sarah > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Sure. I have attached an excel sheet. I have averaged the signal magnitude across 16 blocks of objects, and 16 blocks of scenes, separately. Each block has 8 TRs (TR=2).
The top plot is the data with the default -TR/2 delay. The bottom plot is the data with -2TR delay.
In both plots, we see that the signal drops in the first 2 TRs and then starts rising around TR 3. We would like to see this rise at TR1, that's why we think that we need to shift the onset times. However, when we added the -2TR delay, we still got the same fall and rise. This pattern is consistent across all subjects.
When we were using SPM, we always shifted the signal by 2TRs and always saw the rise at the first TR. I am not sure what I am doing wrong, here.
Appreciate your help.
Thanks,
On Fri, Mar 30, 2018 at 8:09 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
not sure what you are trying to do. can you send a picture? the default lag is TR/2
On 3/29/18 2:30 PM, Sarah Cole wrote:
Thanks, Doug.
I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation.
Do you have any recommendations?
Thanks, Sarah
On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
You can use the -delay flag in mkanalysis-sess
doug
On 03/28/2018 05:35 PM, Sarah Cole wrote:
Hi Doug,
I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks.
We used to shift our raw data by 2 TRs when we were using SPM.
How can we do this in FreeSurfer?
Thank you,
Sarah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Please ignore my previous post. I was wrong on so many levels!
Thanks
S
On Fri, Mar 30, 2018 at 8:34 AM, Sarah Cole coleashley00@gmail.com wrote:
Hi Doug,
Sure. I have attached an excel sheet. I have averaged the signal magnitude across 16 blocks of objects, and 16 blocks of scenes, separately. Each block has 8 TRs (TR=2).
The top plot is the data with the default -TR/2 delay. The bottom plot is the data with -2TR delay.
In both plots, we see that the signal drops in the first 2 TRs and then starts rising around TR 3. We would like to see this rise at TR1, that's why we think that we need to shift the onset times. However, when we added the -2TR delay, we still got the same fall and rise. This pattern is consistent across all subjects.
When we were using SPM, we always shifted the signal by 2TRs and always saw the rise at the first TR. I am not sure what I am doing wrong, here.
Appreciate your help.
Thanks,
On Fri, Mar 30, 2018 at 8:09 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
not sure what you are trying to do. can you send a picture? the default lag is TR/2
On 3/29/18 2:30 PM, Sarah Cole wrote:
Thanks, Doug.
I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation.
Do you have any recommendations?
Thanks, Sarah
On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve <dgreve@mgh.harvard.edu
wrote:
You can use the -delay flag in mkanalysis-sess
doug
On 03/28/2018 05:35 PM, Sarah Cole wrote:
Hi Doug,
I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks.
We used to shift our raw data by 2 TRs when we were using SPM.
How can we do this in FreeSurfer?
Thank you,
Sarah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N. Greve
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Sarah Cole