try what I suggested and see if that helps
On Mon, 3 Jun 2013, Erin Browning
wrote:
Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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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