Re: [Freesurfer] Help with subject's functional overlay

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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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


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