It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). 


On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this  is not an issue I think
doug


On 06/03/2013 02:20 PM, Erin Browning wrote:
We use:

mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz

where freesurfer is our freesurfer subject folder.


On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    what is your mri_convert command line?

    On 06/03/2013 02:11 PM, Erin Browning wrote:
    > Hi everyone--
    >
    > We have a series of scans with an hyperintense artifact cutting
    > through the temporal and frontal lobe. When we run mri_convert to
    > convert from AFNI .BRIK files to .mgz fles, the results look
    like the
    > attached image.
    >
    > How can I correct for this? We tried skullstripping in AFNI first to
    > remove some of the artifact, but that didn't seem to help very much.
    >
    > Thank you,
    > Erin Browning
    >
    >
    >
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