Thanks for your help Doug. That cleared things up. One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity?
Cesar On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > sorry, there should be an fsig.nii.gz which is the F test of the real and > imaginary. That sounds like what you are asking for > > > On 12/04/2013 12:19 PM, Cesar Echavarria wrote: > >> To clarify, I am piggy-backing on the retinotopic analysis to map out >> orientation preference with the travelling-wave method. We presented >> subjects with a rotating grating and right now I am simply interested in >> finding the voxels that have significant activity in response to any >> orientation. Now, when I load the sig.nii file under the 'polar' folder >> with MATLAB I see that each voxel has 2 values. I understand that these are >> the p-values for the real and imaginary components of the signal. Is there >> a way to put these 2 values together for my purposes? Is there a file >> somewhere in the pipeline that will give me the values I am looking for? >> >> Thanks you for your help >> >> Cesar >> >> >> On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> They are compared against 0 (ie, no change from baseline). The >> negatives just mean that the real component was negative >> doug >> >> >> >> On 12/03/2013 06:21 PM, Cesar Echavarria wrote: >> >> >> So I want to figure out which voxels were modulated >> significantly by the orientation of our stimuli. Is this the >> right file to look at? If so what are the real and imaginary >> components compared against? I want to know to make sense of >> the negative values. >> >> On Dec 3, 2013 5:52 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: >> >> It is the -log10(pvalue) where pvalue is the p-value >> from the F-test >> of the real and imaginary components >> doug >> >> >> >> >> >> On 12/03/2013 05:41 PM, Cesar Echavarria wrote: >> > Hi freesurfers, >> > >> > I conducted a retinotopic analysis for one of my >> subjects. I was >> > wondering if any of you knew what is represented by the >> values >> in the >> > sig.nii file under the 'polar' directory that the >> process puts out. >> > >> > I appreciate your help! >> > >> > Cesar >> > >> > >> > _______________________________________________ >> > 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: 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> >> <http://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 >> <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 >> >> >> 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 >> 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/ >> >> >> >> >> -- >> Cesar Echavarria >> Research Assistant >> Martinos Center for Biomedical Imaging, Harvard-MGH >> Brain & Cognitive Sciences | MIT 2012 >> > > -- > 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/ > > -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
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