This file is created when you run reg-feat2anat and should be the one that gets changed with --manxfm func2anat. You can handle this differently if you

1. Manually edit the anat2exf.register.dat so that it is relatively close (no need to be perfect) cd feat/reg/freesurfer tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat --surfs

2. Run bbregister: cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup bbregister --mov ../../example_func.nii.gz --init-reg anat2exf.register.dat --reg anat2exf.register.dat --bold

this second step will fine-tune your hand-edited version. Then go back and run aparc2feat, etc.

doug

Michelle Umali wrote:

Hi Doug, The file that changed was exf2std.register.dat. How do I specify that I wanted that anat2exf.register.dat is supposed to be edited? At what point in the processing stream does this occur?

Did editing exf2std.register.dat do anything?

Thanks. Michelle

On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

The registration that should be used for all of these is
anat2exf.register.dat found in feat/reg/freesurfer. Can you verify
that that was the one that you manually changed? Look at the time
stamp as compared to the other files in that folder.
doug

Michelle Umali wrote:

    Hi Doug,
    I am using reg-feat2anat  on the feat directory of each run.
        reg-feat2anat --feat feadir.feat --subject XX
    Then I checked and adjusted the registration with:
        reg-feat2anat --feat featdir.feat --manual
    Next I checked and adjusted the registration to the standard with:
        reg-feat2anat --feat featdir.feat --manxfm func2std

    To generate cortical binary masks I used:
        aparc2feat --feat featdir.feat --annot BA
        fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10
    -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz

    To generate subcortical binary masks I did:
        aseg2feat --feat featdir.feat --aseg aparc+aseg
        fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz
    -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz

    When I looked at the masks in FSLview and checked the masks
    against the other atlases, everything was off even after
    painstakingly editing the registrations.
    Is there something I am doing wrong?

    Thanks.
    Michelle

       On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

       How are you generating the masks?
       doug

       Michelle Umali wrote:

           Hi Freesurfers,
           I've run reg-feat2anat on several subjects in order to
           generate binary masks to use in an FSL ppi.
           For 3 subjects, this completely failed.

           When I looked at the fsl's own registration of fsl feat 2
           standard (via tkregister2), the registration is fine, but
           after running reg-feat2anat, the registration of the
    feat to
           the freesurfer anatomical and the feat to standard are
           completely off.

           I manually fixed and saved the registration edits via
           reg-feat2anat --manual, but when I generated the masks
    again,
           they were totally wrong still.
           When looking at freesurfer's feat to standard
    registration, it
           looks like all the brains weren't tall enough in the
    saggital
           view.  Am I supposed to stretch the feat brain to fit?

           How can I fix this so that the masks are accurate?

           Thanks.
           Michelle

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