you can try doing the same thing using the -per-session flag. The problem is that it tries to use the motion correction to correct across sessions, which may or may not work doug
On 12/06/2013 12:37 PM, Cesar Echavarria wrote: > I want to do the analysis in native space. I saw in a past thread that > the native space analysis cannot make use of the -per-run flag. Does > this still hold? > If so, is there another way to get fsig.nii file after analyzing each > session separately in native space? > > Thanks for your help! > > Cesar > > > On Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > To get the F test, you will need to put the runs from both > sessions in the same bold folder (and make sure to use -per-run > registration) > doug > > > > > > On 12/5/13 4:42 PM, Cesar Echavarria wrote: >> 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 <mailto: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> >> <mailto: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>> >> <mailto: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>> >> <mailto: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>> >> <mailto: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>> >> <tel: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>> <tel: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: >> 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> >> >> <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>> >> <mailto: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> >> <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/ >> >> >> >> >> -- >> 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 <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 > > > > > -- > 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
