can you see what aseg*.mgz volumes there are in your mri dir? On Thu, 29 May 2008, Sky Raptentsetsang wrote:
Hello, I am re-running edited data through -autorecon2-cp and during the mri_fill script I receive the following error message:
#@# Fill Tue May 27 09:44:29 PDT 2008 /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.956 -0.049 0.061 -5.626; 0.029 1.045 0.352 -16.780; -0.078 -0.277 0.950 31.426; 0.000 0.000 0.000 1.000; mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri/aseg.auto_noCCseg.mgz No such file or directory Linux polaris.v21.med.va.gov 2.6.20-1.2307.fc5 #1 SMP Sun Mar 18 20:58:09 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue May 27 09:44:34 PDT 2008
In this directory there is a aseg.auto_CCseg.mgz file, but no aseg.auto_noCCseg.mgz file. This data was originally processed with FSv4.0.2 and then edited and we upgraded to the latest v4.0.4. Can anyone tell me what the difference between the *_CCseg.mgz and *_noCCseg.mgz file is? and how I can proceed?
Thanks in advance for any help!
Sky Raptentsetsang
Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954
and what version are you running? The easiest thing to do would be to cp aseg.auto.mgz aseg.auto_noCCseg.mgz
then try again. I think Nick fixed this in the current version On Thu, 29 May 2008, Sky Raptentsetsang wrote:
Hi Bruce, I have the following of the specified files in the ../mri dir: aseg.auto.mgz aseg.auto_CCseg.mgz aseg.mgz
Sky
At 04:00 PM 5/29/2008, Bruce Fischl wrote: can you see what aseg*.mgz volumes there are in your mri dir? On Thu, 29 May 2008, Sky Raptentsetsang wrote:
Hello, I am re-running edited data through -autorecon2-cp and during the mri_fill script I receive the following error message: #@# Fill Tue May 27 09:44:29 PDT 2008 /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.956 -0.049 0.061 -5.626; 0.029 1.045 0.352 -16.780; -0.078 -0.277 0.950 31.426; 0.000 0.000 0.000 1.000; mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri/aseg.auto_noCCseg.mgz No such file or directory Linux polaris.v21.med.va.gov 2.6.20-1.2307.fc5 #1 SMP Sun Mar 18 20:58:09 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue May 27 09:44:34 PDT 2008 In this directory there is a aseg.auto_CCseg.mgz file, but no aseg.auto_noCCseg.mgz file. This data was originally processed with FSv4.0.2 and then edited and we upgraded to the latest v4.0.4. Can anyone tell me what the difference between the *_CCseg.mgz and *_noCCseg.mgz file is? and how I can proceed? Thanks in advance for any help! Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954 Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954
the cc gets put into the aseg.auto.mgz I think to create the aseg.auto_CC.mgz or something like that. Nick: is that right?
On Thu, 29 May 2008, Sky Raptentsetsang wrote:
This data was processed with FSv4.0.2, then edited, we upgraded to the latest v4.0.4 and now I am trying to run recon-all with the -autorecon2-cp flag.
I'll try your work around on one of the subjects. Is the aseg.auto_noCCseg.mgz volume usually the same as the aseg.auto.mgz volume? And does this mean that we will lose the CorpusCallosum segmentation for these subjects?
At 04:44 PM 5/29/2008, Bruce Fischl wrote: and what version are you running? The easiest thing to do would be to cp aseg.auto.mgz aseg.auto_noCCseg.mgz
then try again. I think Nick fixed this in the current version On Thu, 29 May 2008, Sky Raptentsetsang wrote: Hi Bruce, I have the following of the specified files in the ../mri dir: aseg.auto.mgz aseg.auto_CCseg.mgz aseg.mgz Sky At 04:00 PM 5/29/2008, Bruce Fischl wrote: can you see what aseg*.mgz volumes there are in your mri dir? On Thu, 29 May 2008, Sky Raptentsetsang wrote: Hello, I am re-running edited data through -autorecon2-cp and during the mri_fill script I receive the following error message: #@# Fill Tue May 27 09:44:29 PDT 2008 /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.956 -0.049 0.061 -5.626; 0.029 1.045 0.352 -16.780; -0.078 -0.277 0.950 31.426; 0.000 0.000 0.000 1.000; mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri/aseg.auto_noCCseg.mgz No such file or directory Linux polaris.v21.med.va.gov 2.6.20-1.2307.fc5 #1 SMP Sun Mar 18 20:58:09 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue May 27 09:44:34 PDT 2008 In this directory there is a aseg.auto_CCseg.mgz file, but no aseg.auto_noCCseg.mgz file. This data was originally processed with FSv4.0.2 and then edited and we upgraded to the latest v4.0.4. Can anyone tell me what the difference between the *_CCseg.mgz and *_noCCseg.mgz file is? and how I can proceed? Thanks in advance for any help! Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954 Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954 Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954
Sky,
The best option for you is to, is Bruce suggests:
cp aseg.auto.mgz aseg.auto_noCCseg.mgz
Nick
On Thu, 2008-05-29 at 19:44 -0400, Bruce Fischl wrote:
and what version are you running? The easiest thing to do would be to cp aseg.auto.mgz aseg.auto_noCCseg.mgz
then try again. I think Nick fixed this in the current version On Thu, 29 May 2008, Sky Raptentsetsang wrote:
Hi Bruce, I have the following of the specified files in the ../mri dir: aseg.auto.mgz aseg.auto_CCseg.mgz aseg.mgz
Sky
At 04:00 PM 5/29/2008, Bruce Fischl wrote: can you see what aseg*.mgz volumes there are in your mri dir? On Thu, 29 May 2008, Sky Raptentsetsang wrote:
Hello, I am re-running edited data through -autorecon2-cp and during the mri_fill script I receive the following error message: #@# Fill Tue May 27 09:44:29 PDT 2008 /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.956 -0.049 0.061 -5.626; 0.029 1.045 0.352 -16.780; -0.078 -0.277 0.950 31.426; 0.000 0.000 0.000 1.000; mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri/aseg.auto_noCCseg.mgz No such file or directory Linux polaris.v21.med.va.gov 2.6.20-1.2307.fc5 #1 SMP Sun Mar 18 20:58:09 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue May 27 09:44:34 PDT 2008 In this directory there is a aseg.auto_CCseg.mgz file, but no aseg.auto_noCCseg.mgz file. This data was originally processed with FSv4.0.2 and then edited and we upgraded to the latest v4.0.4. Can anyone tell me what the difference between the *_CCseg.mgz and *_noCCseg.mgz file is? and how I can proceed? Thanks in advance for any help! Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954 Sky Raptentsetsang Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sky Raptentsetsang