I only have one input. The last posting's orig.jpg was 001.mgz, and motioncor.jpg is orig.mgz. We usually run motioncor because it produces the orig.mgz which has been conformed.
On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what does the 001.mgz look like? Do you have more than one input (otherwise you wouldn't need motion correction)? If so, you'll need to do this for each one
On Mon, 3 Jun 2013, Erin Browning wrote:
The orig.mgz is hyerintense (there's a screenshot of it in another post
now). The AFNI file is in float. I ran:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float --out-scale 1.5 -ns 1
and then I ran motioncor:
recon-all -subjid freesurfer -motioncor
Attached is what the scan looks like after each step; it's still coming out hyperintense like before. I'm concerned it will segment poorly again.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@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 <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<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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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