Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain empty !
Then I followed your recommendation below
recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then
recon-all -s <subjid> -autorecon2 -autorecon3
This produced the result attached.
I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine.
Then I ran recon-all -s <subjid> -autorecon1
This fails with the mri_watershed error.
Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
This runs without error but when I look at the brainmask.mgz it looks just like the attached image.
Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy.
Darren
Hi Darren
can you describe your input data? What format, resolution, etc... is it? If you upload it we'll take a look cheers Bruce On Wed, 5 Sep 2012, Darren Gitelman wrote:
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain empty !
Then I followed your recommendation below
recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then
recon-all -s <subjid> -autorecon2 -autorecon3
This produced the result attached.
I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine.
Then I ran recon-all -s <subjid> -autorecon1
This fails with the mri_watershed error.
Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
This runs without error but when I look at the brainmask.mgz it looks just like the attached image.
Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy.
Darren
Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain empty !
Then I followed your recommendation below
recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then
recon-all -s <subjid> -autorecon2 -autorecon3
This produced the result attached.
I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine.
Then I ran recon-all -s <subjid> -autorecon1
This fails with the mri_watershed error.
Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
This runs without error but when I look at the brainmask.mgz it looks just like the attached image.
Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy.
Darren
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm running it now with the current dev version and it's passed the skull stripping stage and it seems to have worked fine...
On Wed, 5 Sep 2012, Nick Schmansky wrote:
Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain empty !
Then I followed your recommendation below
recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then
recon-all -s <subjid> -autorecon2 -autorecon3
This produced the result attached.
I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine.
Then I ran recon-all -s <subjid> -autorecon1
This fails with the mri_watershed error.
Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
This runs without error but when I look at the brainmask.mgz it looks just like the attached image.
Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy.
Darren
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Darren Gitelman -
Nick Schmansky