Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-24 Thread SHAHIN NASR
Hi Doug,
Sorry to follow this topic with a delay but we tried to model BOLD
signal undershoot with a gamma function and we failed. The problem is,
gamma function generates positive values and we can NOT use inverse gamma
function (or otherfunction similar to that) as a part of mkanalysis-sess
(for modeling BOLD signal undershoot). We even used matlab gammafit to
estimate parameters and it said that values should be positive otherwise
gammafit function fails.
Do you have any suggestion?



On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 yes, that is what you want. The only other way that comes to mind is to
 model each event type as two event types one delayed relative to the other.
 Then model the responseto each as a gamma. If the delay is right, then the
 first gamma should model the main positive response and the second gamma
 will model the negative response. both will be independent from the other.

 doug


 On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:

 I think I figured it out but I want to double check. I am generating
 group-average map for my subjects using isxconcat-sess command which
 generates ces maps for each time frame. I think these maps are what I
 wanted. Right?
 If you still have other solutions that you think may generate more
 reliable results, I am eager to know. For instance, is there anyway to
 fit a model as we do for spmhrf or fslhrf, but just for the negative
 peak?

 Regards

  That's the problem Doug. I have already generated the FIR model but how
 can
 I show the sig MAP for one particulat time point.  What are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu**wrote:

  Hi Shahin, there are several ways that you could do it. The one that
 immediately comes to mind is to use an FIR and then test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

  Hi,
   I want to generate a map to show the significant difference
 between
 HRF undershoot  (negative peak of activity) between two conditions
 independent from the positive peak. Is there anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

  --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs:
 surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
 http://**surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 FileDrop:
 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
 h**ttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 
 Outgoing: ftp://surfer.nmr.mgh.harvard.***
 *edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 




 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School



 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School
 __**_
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-24 Thread Douglas N Greve

What do you mean the gamma function generates positive values? It will 
create a regressor with a positive-going HRF. However, the regression 
coefficient can be negative which would invert the shape. The reg coef 
is fit to the data, so the data will tell you whether there is an 
undershoot or not.
doug


On 04/24/2013 03:02 PM, SHAHIN NASR wrote:
 Hi Doug,
 Sorry to follow this topic with a delay but we tried to model BOLD 
 signal undershoot with a gamma function and we failed. The problem is, 
 gamma function generates positive values and we can NOT use inverse 
 gamma function (or otherfunction similar to that) as a part of 
 mkanalysis-sess (for modeling BOLD signal undershoot). We even used 
 matlab gammafit to estimate parameters and it said that values should 
 be positive otherwise gammafit function fails.
 Do you have any suggestion?



 On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 yes, that is what you want. The only other way that comes to mind
 is to model each event type as two event types one delayed
 relative to the other. Then model the responseto each as a gamma.
 If the delay is right, then the first gamma should model the main
 positive response and the second gamma will model the negative
 response. both will be independent from the other.

 doug


 On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.harvard.edu wrote:

 I think I figured it out but I want to double check. I am
 generating
 group-average map for my subjects using isxconcat-sess command
 which
 generates ces maps for each time frame. I think these maps are
 what I
 wanted. Right?
 If you still have other solutions that you think may
 generate more
 reliable results, I am eager to know. For instance, is there
 anyway to
 fit a model as we do for spmhrf or fslhrf, but just for the
 negative
 peak?

 Regards

 That's the problem Doug. I have already generated the FIR
 model but how
 can
 I show the sig MAP for one particulat time point.  What
 are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.eduwrote:

 Hi Shahin, there are several ways that you could do
 it. The one that
 immediately comes to mind is to use an FIR and then
 test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

 Hi,
   I want to generate a map to show the
 significant difference
 between
 HRF undershoot  (negative peak of activity)
 between two conditions
 independent from the positive peak. Is there
 anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time
 course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
 
 http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School



 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School
 ___
 Freesurfer mailing list
 

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-24 Thread Douglas N Greve
You don't generate a negative coefficient. The sign and magnitude of the 
coefficient is determined by the fitting procedure. It may be the case 
that a positive coef fits the data better than a negative. You should 
not change the gamma parameters.
doug



On 04/24/2013 04:06 PM, SHAHIN NASR wrote:

 I know but how can we generate negative coefficient? To clarify, we 
 use alpha=2, delta=2.25 tau=1.25 to generate default HRF. Using 
 negative values for alpha, delta or tau, does not invert the shape of 
 the curve (HRF).


 On Wed, Apr 24, 2013 at 3:12 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 What do you mean the gamma function generates positive values? It
 will create a regressor with a positive-going HRF. However, the
 regression coefficient can be negative which would invert the
 shape. The reg coef is fit to the data, so the data will tell you
 whether there is an undershoot or not.
 doug



 On 04/24/2013 03:02 PM, SHAHIN NASR wrote:

 Hi Doug,
 Sorry to follow this topic with a delay but we tried to
 model BOLD signal undershoot with a gamma function and we
 failed. The problem is, gamma function generates positive
 values and we can NOT use inverse gamma function (or
 otherfunction similar to that) as a part of mkanalysis-sess
 (for modeling BOLD signal undershoot). We even used matlab
 gammafit to estimate parameters and it said that values should
 be positive otherwise gammafit function fails.
 Do you have any suggestion?



 On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 yes, that is what you want. The only other way that comes
 to mind
 is to model each event type as two event types one delayed
 relative to the other. Then model the responseto each as a
 gamma.
 If the delay is right, then the first gamma should model
 the main
 positive response and the second gamma will model the negative
 response. both will be independent from the other.

 doug


 On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.harvard.edu wrote:

 I think I figured it out but I want to double check. I am
 generating
 group-average map for my subjects using isxconcat-sess
 command
 which
 generates ces maps for each time frame. I think these
 maps are
 what I
 wanted. Right?
 If you still have other solutions that you think may
 generate more
 reliable results, I am eager to know. For instance, is
 there
 anyway to
 fit a model as we do for spmhrf or fslhrf, but just
 for the
 negative
 peak?

 Regards

 That's the problem Doug. I have already generated
 the FIR
 model but how
 can
 I show the sig MAP for one particulat time
 point.  What
 are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.eduwrote:


 Hi Shahin, there are several ways that you
 could do
 it. The one that
 immediately comes to mind is to use an FIR and
 then
 test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

 Hi,
   I want to generate a map to show the
 significant difference
 between
 HRF undershoot  (negative peak of activity)
 between two conditions
 independent from the positive peak. Is there
 anyway, to generate this
 map?

 P.S.: Please note that I need a map and
 not a time
 course graph.


 --
 Shahin Nasr


Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-11 Thread SHAHIN NASR
Sorry that I keep on asking questions but I want to know if using a model
can significantly increase the chance of getting a significant response.
  As far as I see for the positive peak, when I use a model (e.g. gamma
model or spmhrf), I see a more significant response compared to when I use
the FIR model. Is it correct? If true, then the same might be correct for
the negative peak.

P.S.: To be more clear, I am talking about the response maps relative to
the baseline.
On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 yes, that is what you want. The only other way that comes to mind is to
 model each event type as two event types one delayed relative to the other.
 Then model the responseto each as a gamma. If the delay is right, then the
 first gamma should model the main positive response and the second gamma
 will model the negative response. both will be independent from the other.

 doug

 On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:

 I think I figured it out but I want to double check. I am generating
 group-average map for my subjects using isxconcat-sess command which
 generates ces maps for each time frame. I think these maps are what I
 wanted. Right?
 If you still have other solutions that you think may generate more
 reliable results, I am eager to know. For instance, is there anyway to
 fit a model as we do for spmhrf or fslhrf, but just for the negative
 peak?

 Regards

  That's the problem Doug. I have already generated the FIR model but how
 can
 I show the sig MAP for one particulat time point.  What are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu**wrote:

  Hi Shahin, there are several ways that you could do it. The one that
 immediately comes to mind is to use an FIR and then test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

  Hi,
   I want to generate a map to show the significant difference
 between
 HRF undershoot  (negative peak of activity) between two conditions
 independent from the positive peak. Is there anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

  --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs:
 surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
 http://**surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 FileDrop:
 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
 h**ttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 
 Outgoing: ftp://surfer.nmr.mgh.harvard.***
 *edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 




 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School



 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School
 __**_
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



___
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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] Fwd: Comparing HRF undershoots between conditions

2013-04-11 Thread Douglas N Greve

Yes, assuming a shape will give you much more power, at least for the 
individual subject.
doug



On 04/11/2013 02:55 AM, SHAHIN NASR wrote:

 Sorry that I keep on asking questions but I want to know if using a 
 model can significantly increase the chance of getting a significant 
 response.
   As far as I see for the positive peak, when I use a model (e.g. 
 gamma model or spmhrf), I see a more significant response compared to 
 when I use the FIR model. Is it correct? If true, then the same might 
 be correct for the negative peak.

 P.S.: To be more clear, I am talking about the response maps relative 
 to the baseline.

 On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 yes, that is what you want. The only other way that comes to mind
 is to model each event type as two event types one delayed
 relative to the other. Then model the responseto each as a gamma.
 If the delay is right, then the first gamma should model the main
 positive response and the second gamma will model the negative
 response. both will be independent from the other.

 doug

 On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.harvard.edu wrote:

 I think I figured it out but I want to double check. I am
 generating
 group-average map for my subjects using isxconcat-sess command
 which
 generates ces maps for each time frame. I think these maps are
 what I
 wanted. Right?
 If you still have other solutions that you think may
 generate more
 reliable results, I am eager to know. For instance, is there
 anyway to
 fit a model as we do for spmhrf or fslhrf, but just for the
 negative
 peak?

 Regards

 That's the problem Doug. I have already generated the FIR
 model but how
 can
 I show the sig MAP for one particulat time point.  What
 are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.eduwrote:

 Hi Shahin, there are several ways that you could do
 it. The one that
 immediately comes to mind is to use an FIR and then
 test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

 Hi,
   I want to generate a map to show the
 significant difference
 between
 HRF undershoot  (negative peak of activity)
 between two conditions
 independent from the positive peak. Is there
 anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time
 course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
 
 http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School



 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School
 ___
 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
 gr...@nmr.mgh.harvard.edu 

[Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-10 Thread SHAHIN NASR
That's the problem Doug. I have already generated the FIR model but how can
I show the sig MAP for one particulat time point.  What are the other
ways?


On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Hi Shahin, there are several ways that you could do it. The one that
 immediately comes to mind is to use an FIR and then test for a difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

 Hi,
  I want to generate a map to show the significant difference between
 HRF undershoot  (negative peak of activity) between two conditions
 independent from the positive peak. Is there anyway, to generate this map?

 P.S.: Please note that I need a map and not a time course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School



-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
___
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] Fwd: Comparing HRF undershoots between conditions

2013-04-10 Thread Douglas N Greve

yes, that is what you want. The only other way that comes to mind is to 
model each event type as two event types one delayed relative to the 
other. Then model the responseto each as a gamma. If the delay is right, 
then the first gamma should model the main positive response and the 
second gamma will model the negative response. both will be independent 
from the other.

doug

On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:
 I think I figured it out but I want to double check. I am generating
 group-average map for my subjects using isxconcat-sess command which
 generates ces maps for each time frame. I think these maps are what I
 wanted. Right?
 If you still have other solutions that you think may generate more
 reliable results, I am eager to know. For instance, is there anyway to
 fit a model as we do for spmhrf or fslhrf, but just for the negative
 peak?

 Regards

 That's the problem Doug. I have already generated the FIR model but how
 can
 I show the sig MAP for one particulat time point.  What are the other
 ways?


 On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.eduwrote:

 Hi Shahin, there are several ways that you could do it. The one that
 immediately comes to mind is to use an FIR and then test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

 Hi,
   I want to generate a map to show the significant difference
 between
 HRF undershoot  (negative peak of activity) between two conditions
 independent from the positive peak. Is there anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs:
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School



 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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