Hi Erin

that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir)

mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns


this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110.

cheers
Bruce

On Mon, 3 Jun 2013, Erin Browning wrote:

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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    MGH-NMR Center
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--
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
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