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.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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel: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><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><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> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel: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/ > > > > > > -- > 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/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
