Dear FS team,
We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject)
We get the following error: option --ribbon unknown.
The ribbon.mgz folders exist and are located in the right directory. We also tried to re-create them and this worked fine, but again after running the command above we got the same error. If we changed the command --ribbon to -- no ribbon, the script ran, but when we looked at the stats-file, only cortical grey matter labels were segmented (no wm). The same applies to other subjects we tried.
Could you please help us out?
Many thanks. Jolijn & Caroline
What version of FS are you using? You may need a newer version of mri_aparc2aseg. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
On 05/12/2016 06:53 AM, Caroline Beelen wrote:
If we changed the command –-ribbon to –- no ribbon, the script ran, but when we looked at the stats-file, only cortical grey matte
Hi,
This task will be a bit easy using fslmaths
- convert mgz file to nii using mri_convert -then use fslmaths <labeled nii file> -thr <label> -uthr <label> <outputfile.nii>
example: fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii
On Thu, May 12, 2016 at 9:12 AM Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
What version of FS are you using? You may need a newer version of mri_aparc2aseg. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
On 05/12/2016 06:53 AM, Caroline Beelen wrote:
If we changed the command –-ribbon to –- no ribbon, the script ran, but when we looked at the stats-file, only cortical grey matte
-- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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you can also use mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii
On 05/13/2016 06:12 PM, Pradeep wrote:
Hi,
This task will be a bit easy using fslmaths
- convert mgz file to nii using mri_convert
-then use fslmaths <labeled nii file> -thr <label> -uthr <label> <outputfile.nii>
example: fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii
On Thu, May 12, 2016 at 9:12 AM Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What version of FS are you using? You may need a newer version of mri_aparc2aseg. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg On 05/12/2016 06:53 AM, Caroline Beelen wrote: > > If we changed the command –-ribbon to –- no ribbon, the script ran, > but when we looked at the stats-file, only cortical grey matte > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto: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> FileDrop: 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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Caroline Beelen -
Douglas N Greve -
Pradeep