Re: [Freesurfer] Hemodynamic Lag Shift

[Sarah Cole]

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  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 
> 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 > > 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 
>> listfreesur...@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 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.

Re: [Freesurfer] Hemodynamic Lag Shift

[Sarah Cole]

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 
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 
> 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 
> listfreesur...@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.
>
>


HRF_Shift_FSFAST.xlsx
Description: MS-Excel 2007 spreadsheet
___
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.

Re: [Freesurfer] Hemodynamic Lag Shift

[Douglas Greve]

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 
> 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 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.

Re: [Freesurfer] Hemodynamic Lag Shift

[Sarah Cole]

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 
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 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.

Re: [Freesurfer] Hemodynamic Lag Shift

[Douglas N. Greve]

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] Hemodynamic Lag Shift

[Sarah Cole]

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


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.