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.
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.
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. (< DGREVE@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 CautionDear 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.
The information in this e-mail is intended only for the person 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/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.
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. (<DGREVE@mgh.harvard.edumailto:DGREVE@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.
The information in this e-mail is intended only for the person 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/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.
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Greve, Douglas N.,Ph.D. -
Marina Fernández