Probably the easiest thing is just to edit that voxel to be one of the
neighboring segments. First, load the aseg and find that voxel. See which
segment(s) are around that voxel and get the segmentation id. Then run
mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o
aparc+aseg.mgz
then re-run gtmseg
On 10/8/2019 10:34 AM, Marina Fernández wrote:
External Email - Use Caution
I run the command that you told me (mri_binarize --i aseg.presurf.mgz --match
229 --o bin229.mgz) and I get a mask with one voxel.
How can I do to solve it?
Thank you.
Marina.
El lun., 7 oct. 2019 a las 23:19, Greve, Douglas N.,Ph.D.
(<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>) escribió:
We'll have to figure out where those 229s are coming from. Try this
mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz
It should print out whether there were any voxels that matched. If so, you can
load bin229.mgz with the norm.mgz and the aseg.presurf.mgz and see where they
are. If there are not any, then do the same thing with aparc+aseg.mgz
On 10/7/2019 4:54 PM, Marina Fernández wrote:
External Email - Use Caution
Dear Douglas,
Sorry! This is the previous information:
> Dear Douglas,
>
> Thank you for the replay.
>
> I think so, I can't find the code 229 in any subject.
>
> I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have
> the normal > > segmentation and labels. Could it be a problem with the
> extracerebral voxels?
>
> Best regards,
> Marina.
> That is kind of weird. It says it has found a segmentation with number
> 229, but we don't have that code in our system. Can you find the 229 voxels
> in the aparc+aseg.mgz?
> Dear experts,
>
> The following error occurs with one subject when I am running gtmseg
> command:
>
> Computing colortable
> ERROR: cannot find match for subcortical segid 229
> ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
> apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo
> gtmseg existed with errors
> ans=1
>
> Do you know what happened with this subject? What can I do to solve it?
>
> Thank you very much in advance.
> Marina.
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