[Freesurfer] error loading volume brainmask.gcut.mgz
Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0. 93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1. 93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
yes I did answer again to the list. no it is no full at all. 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading volume brainmask.gcut.mgz
and my freesurfer version is 5.1. 2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com yes I did answer again to the list. no it is no full at all. 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = -0., c_r = 8.4909 : x_a = -0., y_a = 0., z_a = 1., c_a = -0.4031 : x_s = 0., y_s = -1., z_s = -0., c_s = -34.1638 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. -0. 136.4909 -0. 0. 1. -128.4031 0. -1. -0.93.8362 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 136.4909 -0. -0. -1.93.8362 -0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote: Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
