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 <gr...@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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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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