Hi Doug,
Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4
Thank you, Kaley
Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer@nmr.mgh.harvard.edu Message-ID: 02f67013-f90c-699f-0307-9f1bf9b131be@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
what is your freeview command?
On 6/14/17 3:51 PM, KALEY E ELLIS wrote:
Dear FreeSurfer Developers,
We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6.
We are going through the manual editing process and are checking the brainmask by following these instructions:
We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors:
reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... reading input surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... reading input white surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... INFO: assuming MGZ format for volumes.
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
277 173 970 3.493 0.659 0.107 0.039 3 0.4 ./rh.entorhinal_exvivo.label
#------------------------------------------
Started at Thu Jun 8 10:50:24 CDT 2017 Ended at Fri Jun 9 00:06:58 CDT 2017 #@#%# recon-all-run-time-hours 13.276 recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017
Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem.
Thank you!
Kaley
Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Hi Doug,
We are still experiencing problems with this issue. However, we are now also seeing it with the WM layer.
Our freeview command to look at the brainmask is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4
Our freeview command to do the WM manual edits is: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red
Thank you, Kaley
Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer@nmr.mgh.harvard.edu Message-ID: 02f67013-f90c-699f-0307-9f1bf9b131be@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
what is your freeview command?
On 6/14/17 3:51 PM, KALEY E ELLIS wrote:
Dear FreeSurfer Developers,
We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6.
We are going through the manual editing process and are checking the brainmask by following these instructions:
We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors:
reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... reading input surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... reading input white surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... INFO: assuming MGZ format for volumes.
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
277 173 970 3.493 0.659 0.107 0.039 3 0.4 ./rh.entorhinal_exvivo.label
#------------------------------------------
Started at Thu Jun 8 10:50:24 CDT 2017 Ended at Fri Jun 9 00:06:58 CDT 2017 #@#%# recon-all-run-time-hours 13.276 recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017
Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem.
Thank you!
Kaley
Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
I'm not sure what is going on here as the T1.mgz and the brainmask.mgz should be in same space. Can you run mri_info on both of them and send me the result? Can you also make sure that T1.mgz is older than the brainmask?
On 6/27/17 11:49 AM, KALEY E ELLIS wrote:
Hi Doug,
We are still experiencing problems with this issue. However, we are now also seeing it with the WM layer.
Our freeview command to look at the brainmask is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4
Our freeview command to do the WM manual edits is: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red
Thank you, Kaley
Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer@nmr.mgh.harvard.edu Message-ID: 02f67013-f90c-699f-0307-9f1bf9b131be@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
what is your freeview command?
On 6/14/17 3:51 PM, KALEY E ELLIS wrote:
Dear FreeSurfer Developers,
We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6.
We are going through the manual editing process and are checking the brainmask by following these instructions:
We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors:
reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... reading input surface
/study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... reading input white surface
/study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
INFO: assuming MGZ format for volumes.
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
277 173 970 3.493 0.659 0.107 0.039 3 0.4 ./rh.entorhinal_exvivo.label
#------------------------------------------
Started at Thu Jun 8 10:50:24 CDT 2017 Ended at Fri Jun 9 00:06:58 CDT 2017 #@#%# recon-all-run-time-hours 13.276 recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017
Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem.
Thank you!
Kaley
Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
KALEY E ELLIS