Hi All,
I'm trying to extract signal from an ROI in an analysis that I specified as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce an output file that gives me a single value for each participant. What I'm trying to do is to get a value for each TR in the time window I specified so that I can generate a time course for that ROI. I know that this was possible with the older analysis tools in the older version of freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are just giving me a single (presumably averaged) value. Does anyone know how I can get a timecourse for my ROI?
Thanks, Joe
_________________________________
Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________
It is still possible but not quite as easy. You have to create a contrast for each tap in the FIR, then run funcroi for each tap. doug
On 10/14/14 7:02 PM, Joseph Andreano wrote:
Hi All,
I'm trying to extract signal from an ROI in an analysis that I specified as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce an output file that gives me a single value for each participant. What I'm trying to do is to get a value for each TR in the time window I specified so that I can generate a time course for that ROI. I know that this was possible with the older analysis tools in the older version of freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are just giving me a single (presumably averaged) value. Does anyone know how I can get a timecourse for my ROI?
Thanks, Joe
Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Joe, I assume that you have already 1) defined your FIR function (mkanalysis-sess) and applied it (selxavg3-sess). I also assume that you have already defined your ROIs (funcroi-config) and applied them (funcroi-sess). Up to this point, everything is more or less easy. Now, you want to know how to get your time course! You have to use funcroi-table-sess command multiple times! For FIR analysis, you have to add '-frame X' to your funcroi-table-sess command with X referring to the point in your time course (use funcroi-table-sess --help for more help). You have to repeat this command for each TR in your time course. For example if you have 10 TR, then you have to repeat it 10 times with '-frame 0' to '-frame 9'. Please note that, you have to save the results in 10 different files and then read them later somehow (I use matlab for that) and combine them to make your time course.
Let me know if you faced a problem Good Luck
On Tue, Oct 14, 2014 at 10:24 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It is still possible but not quite as easy. You have to create a contrast for each tap in the FIR, then run funcroi for each tap. doug
On 10/14/14 7:02 PM, Joseph Andreano wrote:
Hi All,
I'm trying to extract signal from an ROI in an analysis that I specified as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce an output file that gives me a single value for each participant. What I'm trying to do is to get a value for each TR in the time window I specified so that I can generate a time course for that ROI. I know that this was possible with the older analysis tools in the older version of freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are just giving me a single (presumably averaged) value. Does anyone know
how
I can get a timecourse for my ROI?
Thanks, Joe
Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Joseph Andreano -
SHAHIN NASR