it keeps having trouble with the aseg volume:
[amc@amcpacs mri]$ recon-all -subjid 1768-4 -edit_wm_with_aseg INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ~/freesurfer_new/freesurfer/subjects/1768-4 Using mgz format --------------------------------------- Editing WM with SubCort Seg Tue Aug 23 14:01:38 EDT 2005 mri_edit_wm_with_aseg wm.mgz aseg.mgz wm.mgz zcat: /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz.gz: No such file or directory mghRead(/home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz, -1): read error mri_edit_wm_with_aseg: could not read aseg volume from aseg.mgz reading wm segmentation from wm.mgz... ERROR: mri_edit_wm_with_aseg with non-zero status recon-all exited with errors at Tue Aug 23 14:01:40 EDT 2005
It cannot find any aseg.mgz volume. I dont have one, just a blank directory called aseg that was made with mksubjdirs process. I dont know where this aseg.mgz would/should have been created?
dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu
"Brian T. Quinn" btquinn@nmr.mgh.harvard.edu 08/23/05 2:08 PM >>>
mri_edit_wm_with_aseg
or
recon-all -edit_wm_with_aseg (if it's in your version of recon-all -> grep for it.)
On Tue, 23 Aug 2005, David Soscia wrote:
thats great, however when I type in the command, the computer is not recognizing it:
[amc@amcpacs mri]$ mri_edit_with_aseg wm aseg wm mri_edit_with_aseg: Command not found.
tried this way also:
[amc@amcpacs mri]$ recon-all -subjid 1768-4 -mri_edit_with_aseg wm
aseg
wm ERROR: Flag -mri_edit_with_aseg unrecognized.
any ideas why?
dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu
Bruce Fischl fischl@nmr.mgh.harvard.edu 08/23/05 1:45 PM >>>
yes, most of that (not fornix or optic nerve)
On Tue, 23 Aug 2005, David Soscia wrote:
Guys,
If you run the auto segmentation editor in the new program, does it
do
the defect editing (optical nerve, fornix, lateral ventricle, basal ganglia) for you, eliminating the time it takes to do this? If this
is
true, it is a life (and time) saver for me.
Dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu _______________________________________________ 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
hi David-
the subcortical segmentation tools have not been released (soon though - early sept.). the -segmentation flag is for the wm segmentation and creates the wm(or wm.mgz) volume. you still have to edit the wm volume in the current release.
thanks, brian
On Tue, 23 Aug 2005, David Soscia wrote:
it keeps having trouble with the aseg volume:
[amc@amcpacs mri]$ recon-all -subjid 1768-4 -edit_wm_with_aseg INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ~/freesurfer_new/freesurfer/subjects/1768-4 Using mgz format
Editing WM with SubCort Seg Tue Aug 23 14:01:38 EDT 2005 mri_edit_wm_with_aseg wm.mgz aseg.mgz wm.mgz zcat: /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz.gz: No such file or directory mghRead(/home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz, -1): read error mri_edit_wm_with_aseg: could not read aseg volume from aseg.mgz reading wm segmentation from wm.mgz... ERROR: mri_edit_wm_with_aseg with non-zero status recon-all exited with errors at Tue Aug 23 14:01:40 EDT 2005
It cannot find any aseg.mgz volume. I dont have one, just a blank directory called aseg that was made with mksubjdirs process. I dont know where this aseg.mgz would/should have been created?
dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu
"Brian T. Quinn" btquinn@nmr.mgh.harvard.edu 08/23/05 2:08 PM >>>
mri_edit_wm_with_aseg
or
recon-all -edit_wm_with_aseg (if it's in your version of recon-all -> grep for it.)
On Tue, 23 Aug 2005, David Soscia wrote:
thats great, however when I type in the command, the computer is not recognizing it:
[amc@amcpacs mri]$ mri_edit_with_aseg wm aseg wm mri_edit_with_aseg: Command not found.
tried this way also:
[amc@amcpacs mri]$ recon-all -subjid 1768-4 -mri_edit_with_aseg wm
aseg
wm ERROR: Flag -mri_edit_with_aseg unrecognized.
any ideas why?
dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu
Bruce Fischl fischl@nmr.mgh.harvard.edu 08/23/05 1:45 PM >>>
yes, most of that (not fornix or optic nerve)
On Tue, 23 Aug 2005, David Soscia wrote:
Guys,
If you run the auto segmentation editor in the new program, does it
do
the defect editing (optical nerve, fornix, lateral ventricle, basal ganglia) for you, eliminating the time it takes to do this? If this
is
true, it is a life (and time) saver for me.
Dave
David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad@mail.amc.edu _______________________________________________ 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
-- brian t. quinn
freesurfer@nmr.mgh.harvard.edu
-
Brian T. Quinn -
David Soscia