I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go.
Also, they are only used in event related and AB designs, not blocked, correct?
Katie
FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR.
doug
Katie Bettencourt wrote:
I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go.
Also, they are only used in event related and AB designs, not blocked, correct?
Katie
Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights....
I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine.
I'm very confused here.
Also, is there a difference between the way this is used in FIR and Gamma analyses?
Katie
On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR.
doug
Katie Bettencourt wrote:
I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go.
Also, they are only used in event related and AB designs, not blocked, correct?
Katie
-- 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/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Oh, sorry, I had forgotten when I introduced the 4col format. Yes, 4.5 does take the 4 col. I actually dont remember exactly what 4.5 does when you give it autostimdur with a 4col. It might ignore the duration in the parfile and compute it from the stimulus timing. If you represent all time in your paradigm file, this should do the same thing. For the FIR, the stimulus duration is ignored entirely.
doug
Katie Bettencourt wrote:
Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights....
I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine.
I'm very confused here.
Also, is there a difference between the way this is used in FIR and Gamma analyses?
Katie
On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR. doug Katie Bettencourt wrote: I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 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> 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.
Ok, so if I use the 4 col I don't need to use -autostimdur, I can use -noautostimdur or can I leave it out all together?
I noticed that FIR ignored the stimulus duration entirely, so I only need the -autostimdur/noautostimdur for gamma event related or AB designs?
However, I did get a difference (and a fairly large one) for a FIR event related analysis with 4 col paradigm files when I did mkanalysis-sess -noautostimdur and mkanalysis-sess -autostimdur. Should i just ignore the -autostimdur one?
Katie
On Fri, Apr 15, 2011 at 2:51 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Oh, sorry, I had forgotten when I introduced the 4col format. Yes, 4.5 does take the 4 col. I actually dont remember exactly what 4.5 does when you give it autostimdur with a 4col. It might ignore the duration in the parfile and compute it from the stimulus timing. If you represent all time in your paradigm file, this should do the same thing. For the FIR, the stimulus duration is ignored entirely.
doug
Katie Bettencourt wrote:
Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights....
I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine.
I'm very confused here.
Also, is there a difference between the way this is used in FIR and Gamma analyses?
Katie
On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR.
doug
Katie Bettencourt wrote:
I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 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
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.
-- 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/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Katie Bettencourt wrote:
Ok, so if I use the 4 col I don't need to use -autostimdur, I can use -noautostimdur or can I leave it out all together?
I think it forces you to choose one. If you have 4 col, then use -noautostimdur
I noticed that FIR ignored the stimulus duration entirely, so I only need the -autostimdur/noautostimdur for gamma event related or AB designs?
FIR will ignore the duration. For gammafit, the duration is important, but if you have 4col, then use -no-autostimdur. For AB, there is no paradigm file -- you tell it the on and off durations.
However, I did get a difference (and a fairly large one) for a FIR event related analysis with 4 col paradigm files when I did mkanalysis-sess -noautostimdur and mkanalysis-sess -autostimdur. Should i just ignore the -autostimdur one?
Yes, ignore the -autostimdur.
doug
Katie
On Fri, Apr 15, 2011 at 2:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Oh, sorry, I had forgotten when I introduced the 4col format. Yes, 4.5 does take the 4 col. I actually dont remember exactly what 4.5 does when you give it autostimdur with a 4col. It might ignore the duration in the parfile and compute it from the stimulus timing. If you represent all time in your paradigm file, this should do the same thing. For the FIR, the stimulus duration is ignored entirely. doug Katie Bettencourt wrote: Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights.... I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine. I'm very confused here. Also, is there a difference between the way this is used in FIR and Gamma analyses? Katie On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR. doug Katie Bettencourt wrote: I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 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> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 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>
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