Re: [Freesurfer] Fwd: mir_convert produces a darkened file

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