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 greve@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 greve@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/
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 greve@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 greve@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
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, shahin@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 greve@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 greve@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
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" greve@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, shahin@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 greve@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 differencebetween 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 greve@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 greve@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/
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" <greve@nmr.mgh.harvard.edu mailto:greve@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, shahin@nmr.mgh.harvard.edu <mailto:shahin@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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/BugReporting><http://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.html><http://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 greve@nmr.mgh.harvard.edu <mailto:greve@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/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 greve@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, shahin@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 greve@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 differencebetween 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 greve@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 greve@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/
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 <greve@nmr.mgh.harvard.edu mailto:greve@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, shahin@nmr.mgh.harvard.edu <mailto:shahin@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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/BugReporting><http://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.html><http://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 greve@nmr.mgh.harvard.edu <mailto:greve@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/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
SHAHIN NASR -
shahin＠nmr.mgh.harvard.edu