It looks like it is the 1st regressor. Although there appears to be a period of time where this is no button press. If the button press is the only event, then it is definitely the 1st regressor. Note that all runs are concatenated together. doug On 07/16/2013 12:17 PM, Nicholas Paul Denisuk wrote:
Freesurfer Users,
Here is the X.mat file. Thank you!
Nick Denisuk
On 7/16/13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the X.mat file?
On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote:
Dear Freesurfer Users,
I have opened up the X.mat file from the analysis. I think that the button regressor is the third column in the file, but I am not 100% sure. Do you know which column the button regressor is? Below is the background info to this question.
I am trying to regress out the activity associated with button presses
in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)?
Thanks you,
Nick
Hi Nick, please remember to post to the list and not to us personally.
To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work.
doug _______________________________________________ Freesurfer mailing list 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 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/
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Freesurfer Users,
I am attempting to run a retinotopy analysis where I regress out button presses. When I run my mkanalysis command, I keep getting the error: -nuisreg requires two arguments. My command line is as follows:
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2.6 -retinotopy 55.4666 -paradigm rtopy.par -nuisreg button_regressor_lh -gammafit 2.25 1.25 -polyfit 2 -mcextreg -fwhm 3 -fsd bold_nopace -rlf retino_runs.txt
The "button_regressor_lh" is the text file I created from copying the first column of the X.mat file. I apologize if this is a basic question, but this is my first time running a retinotopic analysis.
Thank You,
Nick
On 7/16/13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It looks like it is the 1st regressor. Although there appears to be a period of time where this is no button press. If the button press is the only event, then it is definitely the 1st regressor. Note that all runs are concatenated together. doug On 07/16/2013 12:17 PM, Nicholas Paul Denisuk wrote:
Freesurfer Users,
Here is the X.mat file. Thank you!
Nick Denisuk
On 7/16/13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the X.mat file?
On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote:
Dear Freesurfer Users,
I have opened up the X.mat file from the analysis. I think that the button regressor is the third column in the file, but I am not 100% sure. Do you know which column the button regressor is? Below is the background info to this question.
I am trying to regress out the activity associated with button presses
in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)?
Thanks you,
Nick
Hi Nick, please remember to post to the list and not to us personally.
To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work.
doug _______________________________________________ Freesurfer mailing list 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 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.
-- 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: 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/
you need to tell it the number of regressors to use. Since you only have one regressor, just put 1 doug
On 07/17/2013 04:00 PM, Nicholas Paul Denisuk wrote:
Freesurfer Users,
I am attempting to run a retinotopy analysis where I regress out button presses. When I run my mkanalysis command, I keep getting the error: -nuisreg requires two arguments. My command line is as follows:
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2.6 -retinotopy 55.4666 -paradigm rtopy.par -nuisreg button_regressor_lh -gammafit 2.25 1.25 -polyfit 2 -mcextreg -fwhm 3 -fsd bold_nopace -rlf retino_runs.txt
The "button_regressor_lh" is the text file I created from copying the first column of the X.mat file. I apologize if this is a basic question, but this is my first time running a retinotopic analysis.
Thank You,
Nick
On 7/16/13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It looks like it is the 1st regressor. Although there appears to be a period of time where this is no button press. If the button press is the only event, then it is definitely the 1st regressor. Note that all runs are concatenated together. doug On 07/16/2013 12:17 PM, Nicholas Paul Denisuk wrote:
Freesurfer Users,
Here is the X.mat file. Thank you!
Nick Denisuk
On 7/16/13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the X.mat file?
On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote:
Dear Freesurfer Users,
I have opened up the X.mat file from the analysis. I think that the button regressor is the third column in the file, but I am not 100% sure. Do you know which column the button regressor is? Below is the background info to this question.
> I am trying to regress out the activity associated with button > presses
in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)?
Thanks you,
Nick
> Hi Nick, please remember to post to the list and not to us > personally.
To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work.
doug _______________________________________________ Freesurfer mailing list 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 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.
-- 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: 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@nmr.mgh.harvard.edu
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Douglas N Greve -
Nicholas Paul Denisuk