[Freesurfer] Normalization problem
I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control points. This works if I add enough points across the brain ( over 200), and I get a better normalization result after running "recon-all -normalization -usecontrolpoints" and another skull-stripping on the new T1-volume. To test whether or not this produces a good segmentaition of white matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with the segmentation result, I move on to the surface processing stage, and run the -autorecon2 -script. The problem is that after running the -autorecon2, the normalization is completely wrong again, looking more like the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Normalization problem
Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control points. This works if I add enough points across the brain ( over 200), and I get a better normalization result after running "recon-all -normalization -usecontrolpoints" and another skull-stripping on the new T1-volume. To test whether or not this produces a good segmentaition of white matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with the segmentation result, I move on to the surface processing stage, and run the -autorecon2 -script. The problem is that after running the -autorecon2, the normalization is completely wrong again, looking more like the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway. ___ 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] warning
Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer mailing list and google
Dear freesurfer users, By adding the following phrase to google's search box, you can search the freesurfer mailing list archives. site:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ I have found this extremely useful. Satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] warning
don't worry about it - we're taking it out. Bruce On Mon, 21 Nov 2005, Sasha Wolosin wrote: Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ 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] mri_convert problem?
I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz reading from /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img... INFO: analyzeRead(): min = 0, max = 1000 TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.027317, -0.986145, 0.163619) j_ras = (0.0506652, -0.164836, -0.985019) k_ras = (-0.998342, 0.018618, -0.054466) writing to /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... gzip: stdout: Operation not permitted Broken pipe --- Is this a problem with mri_convert or am I doing something wrong that's preventing mri_convert from working properly? Thanks, - Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Normalization problem
Hi, I've encountered similar problems. Do you know if it's specific to the autorecon2 flag? I'm wondering if running each process separately and sequentially get around it, e.g, running recon-all -normalization2, then recon-all -segmentation, then recon-all -fill, etc... Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Bruce Fischl Sent: Mon 21/11/2005 11:03 PM To: Martin Ystad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Normalization problem Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: > I'm working on the latest developmental release for Rh. 9. and I'm > having problems with the normalization procedures on my datasets. > My datasets have large intensity inhomogeneities due to their > acquisition with a surface coil (8-ch. GE). > To fix this problem I have resorted to the use of control points. This > works if I add enough points across the brain ( over 200), and I get a > better normalization result after running "recon-all -normalization > -usecontrolpoints" and another skull-stripping on the new T1-volume. > To test whether or not this produces a good segmentaition of white > matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with > the segmentation result, I move on to the surface processing stage, and > run the -autorecon2 -script. > The problem is that after running the -autorecon2, the normalization is > completely wrong again, looking more like the first normalization done > without control points, and the wm.mgz -volume is also bad. So are the > surfaces. > How do I make freesurfer produce the same good results as I got during > the first normalization? Do I need to specify the use of control points > again, even though the brain.mgz volume looks ok? > > Thanks, > > Martin Ystad > Medical Student > University of Bergen > Institute of Biomedicine > Jonas Lies vei 91, 5009 > Bergen, Norway. > > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem?
does the output dir exists? Do you have write permission? On Mon, 21 Nov 2005, Daniel Goldman wrote: I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz reading from /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img... INFO: analyzeRead(): min = 0, max = 1000 TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.027317, -0.986145, 0.163619) j_ras = (0.0506652, -0.164836, -0.985019) k_ras = (-0.998342, 0.018618, -0.054466) writing to /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... gzip: stdout: Operation not permitted Broken pipe --- Is this a problem with mri_convert or am I doing something wrong that's preventing mri_convert from working properly? Thanks, - Daniel ___ 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
