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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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