Hi Bruce, After unpacking the data, I simply run the selxavg command below and allow it to do the automatic pre-processing.
selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh The analysis was generated with the following command: mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface fsaverage rh -fwhm 5 -paradigm LOC.par -event-related -polyfit 1 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 2 -refeventdur 16 -per-run -force -fsd bold After fixing up the registration I saved the registration file under :Subjects/myla/bold/014/register.dof6.dat" and ran bbregister for all the runs within the subject folder as below. bbregister --mov Subjects/myla/bold/015/f.nii --reg Subjects/myla/bold/015/register.dof6.dat --init-reg Subjects/myla/bold/014/register.dof6.dat --bold I then ran the selxavg3-sess again. Let me know if you need any more information to help. Thanks! Cesar On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Cesar > > what command lines did you run to register and sample? > > Bruce > > On Mon, 5 May 2014, Cesar Echavarria wrote: > > Hello freesurfer experts, >> The functional overlay for one of our subjects looks like the image >> attached. You'll notice >> the "holes" on the overlay that have a value of 0. I'm trying to get ride >> of these as I >> expect (as with other subjects) to have values for these vertices that >> are not 0. Myself and >> a colleague have tried improving the registration as much as we see >> possible, but the problem >> remains. Any tips on how to correct this issue would be greatly >> appreciated. >> >> Thanks in advance for your help! >> [cleardot.gif] >> Cesar Echavarria >> Research AssistantMartinos Center for Biomedical Imaging, Harvard-MGH >> >> Brain & Cognitive Sciences | MIT 2012 >> >> > _______________________________________________ > 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. > > -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
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