Re: [Freesurfer] process volume again
As you have discovered, when using mgz format, the orig.mgz should be in the mri dir. If you have multiple runs, then they should go under mri/orig/001.mgz ... don't know about the seg fault. doug David Soscia wrote: Thanks, after a little tweaking, I managed to get part of the process going. A few things I thought I would mention though... 1. At first when I tried to do the -nuintensitycor command it was saying it found no data in /mri (no orig.mgz file there). When I did mksubjdirs, it made folders for all of the steps (orig, T1, wm, brain, etc) And then when I did a conversion to mgz from dicom of my orig files, they went into my orig folder, ie. mri/orig/orig.mgz. Maybe I did the conversion wrong so it sent it there instead of in the mri directory, however I thought the purpose of the mksibjdirs was to make seperate folders to put the seperate steps into. After I saw this error message in the -nuintensitycor process, I moved the orig.mgz file from the orig directory into the mri directory and it worked fine. 2. When I run the next step, -normalization, I am getting an error half way through... [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -normalization -mgz 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### Using mgz format - Intensity Normalization Mon Aug 22 09:14:14 EDT 2005 /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Mon Aug 22 09:15:16 EDT 2005 Any ideas on what the problems could be? Thanks for your help so far. 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 [EMAIL PROTECTED] "Brian T. Quinn" <[EMAIL PROTECTED]> 08/20/05 3:49 PM >>> hi Dave- it sounds like you may be skipping some steps. what volume do you currently have? the order of the volumes to be created is: orig->nu->T1->brain->wm the -segmentation step only runs the brain->wm step. if you have an orig volume, use either: -stage1 or: -nuintensitycor -normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: hey guys, Now I am getting this error when trying to process the volume: [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### Using mgz format - Segmentation Fri Aug 19 13:30:42 EDT 2005 ERROR: cannot find brain.mgz recon-all exited with er
Re: [Freesurfer] process volume again
Thanks, after a little tweaking, I managed to get part of the process going. A few things I thought I would mention though... 1. At first when I tried to do the -nuintensitycor command it was saying it found no data in /mri (no orig.mgz file there). When I did mksubjdirs, it made folders for all of the steps (orig, T1, wm, brain, etc) And then when I did a conversion to mgz from dicom of my orig files, they went into my orig folder, ie. mri/orig/orig.mgz. Maybe I did the conversion wrong so it sent it there instead of in the mri directory, however I thought the purpose of the mksibjdirs was to make seperate folders to put the seperate steps into. After I saw this error message in the -nuintensitycor process, I moved the orig.mgz file from the orig directory into the mri directory and it worked fine. 2. When I run the next step, -normalization, I am getting an error half way through... [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -normalization -mgz 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### Using mgz format - Intensity Normalization Mon Aug 22 09:14:14 EDT 2005 /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Mon Aug 22 09:15:16 EDT 2005 Any ideas on what the problems could be? Thanks for your help so far. 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 [EMAIL PROTECTED] >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 08/20/05 3:49 PM >>> hi Dave- it sounds like you may be skipping some steps. what volume do you currently have? the order of the volumes to be created is: orig->nu->T1->brain->wm the -segmentation step only runs the brain->wm step. if you have an orig volume, use either: -stage1 or: -nuintensitycor -normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: > hey guys, > > Now I am getting this error when trying to process the volume: > > [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation > 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 $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ### > Using mgz format > - > Segmentation Fri Aug 19 13:30:42 EDT 2005 > ERROR: cannot find brain.mgz > recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 > > > i dont have a brain.mgz in the brain directory because I thought the > purpose of this process was to create it. Any suggestions? > > Dave > > David A. S
Re: [Freesurfer] process volume again
hi Dave- it sounds like you may be skipping some steps. what volume do you currently have? the order of the volumes to be created is: orig->nu->T1->brain->wm the -segmentation step only runs the brain->wm step. if you have an orig volume, use either: -stage1 or: -nuintensitycor -normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: hey guys, Now I am getting this error when trying to process the volume: [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### Using mgz format - Segmentation Fri Aug 19 13:30:42 EDT 2005 ERROR: cannot find brain.mgz recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 i dont have a brain.mgz in the brain directory because I thought the purpose of this process was to create it. Any suggestions? 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 [EMAIL PROTECTED] ___ 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
Re: [Freesurfer] process volume again
Not sure what's going on there. You may have gotten into a situation where some of the processing was done in COR and some im MGZ. It will assume to do things in mgz unless you specify -COR. One thing you can do to get things synched back up is to convert all your CORs to mgzs, eg, cd mri mri_convert brain brain.mgz doug David Soscia wrote: hey guys, Now I am getting this error when trying to process the volume: [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### Using mgz format - Segmentation Fri Aug 19 13:30:42 EDT 2005 ERROR: cannot find brain.mgz recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 i dont have a brain.mgz in the brain directory because I thought the purpose of this process was to create it. Any suggestions? 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 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] process volume
It automatically tries to figure out what format you use for your analysis. It looks for mri/orig/XXX.mgz (which XXX is anything between 0-9). If it does not find that, it assumes COR. Specify -mgz to force mgz. David Soscia wrote: hey guys, Im trying to process an orig scan from the terminal line: [EMAIL PROTECTED] orig]$ recon-all -subjid 1768-4 -segmentation 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 COR format - Segmentation Thu Aug 18 14:30:56 EDT 2005 ERROR: cannot find brain/COR-.info recon-all exited with errors at Thu Aug 18 14:30:56 EDT 2005 Notice how it says "using COR format." The file I am trying to convert is in mgz format, using the new freesurfer version. I'm confused as to why it is doing this. Thanks, 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 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
