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.eduwrote:
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.**edugreve@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 artifactcutting > 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.eduFreesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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.**htmlhttp://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/
______________________________**_________________ 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> The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
