I used the command below to check the brain mask relative to the subject's anatomy:
tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz The mask looked fine in that no portion of the brain appeared to lie outside the mask. Cesar On Mon, May 5, 2014 at 3:43 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > It could be that the brain mask is too aggressive. Try looking at > Subjects/myla/bold/RRR/masks/brain.nii.gz > > doug > > > > On 05/05/2014 03:17 PM, Cesar Echavarria wrote: > >> 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<mailto: >> 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 <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. >> >> >> >> >> -- >> 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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