Hi Doug,

Me and Shahin have looked at the registration and it looks fine. I know the activation is 0 because when I click on those vertices it tells me the tksconcat.nii value is "**0.000000**". I looked at the cortex.label file and found the 0-valued vertices within the file. We have scanned the same subject for different experiments but it is only for this session that we find the problem. Let me know if there's anything else we can check.

Thanks!
Cesar


On Mon, May 5, 2014 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Have you checked the registration? If so, are you sure that the activation is exactly 0? Also, look at cortex.label to check whether somehow those vertices were not labeled.


On 05/05/2014 04:08 PM, Cesar Echavarria wrote:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@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
        <fischl@nmr.mgh.harvard.edu
        <mailto:fischl@nmr.mgh.harvard.edu>
        <mailto: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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        --         Cesar Echavarria
        Research Assistant
        Martinos Center for Biomedical Imaging, Harvard-MGH
        Brain & Cognitive Sciences | MIT 2012


    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
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    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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    Outgoing:
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--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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