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<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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>> >
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>> >
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>
>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> >
>> FileDrop:
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>>
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>
>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> >
>> Outgoing:
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
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>> >
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop:
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
>>
>>
>>
>>
<<attachment: 1029-ar2.jpg>>
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