I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
well that certainly looks wrong. What does the original image look like? On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
The original image is attached - Even after notal-check, the recon exits with error mri_watershed Error:
GLOBAL region of the brain empty ! \ (we have not included cerebellum fully in the slices: is this a problem?) Thanks for your help
On 08/07/2010 16:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
well that certainly looks wrong. What does the original image look like? On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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.
_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Hi Lena,
-notal-check will disable the error detection, not the tal itself, so won't help in cases where the xform is truly wrong. The image you sent looks PD/T2* weighted, which won't work for the talairaching we use (or for many of our analysis steps).Do you have a T1-weighted image?
cheers Bruce
On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
The original image is attached - Even after notal-check, the recon exits with error mri_watershed Error:
GLOBAL region of the brain empty ! \ (we have not included cerebellum fully in the slices: is this a problem?) Thanks for your help
On 08/07/2010 16:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
well that certainly looks wrong. What does the original image look like? On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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.
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Dear Bruce
We are trying to obtain a good contrast in 7T for thickness measurements using freesurfer by piloting different sequences, is there anyway we can process the T2*s in the pipeline?
On 08/07/2010 17:07, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Lena,
-notal-check will disable the error detection, not the tal itself, so won't help in cases where the xform is truly wrong. The image you sent looks PD/T2* weighted, which won't work for the talairaching we use (or for many of our analysis steps).Do you have a T1-weighted image?
cheers Bruce
On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
The original image is attached - Even after notal-check, the recon exits with error mri_watershed Error:
GLOBAL region of the brain empty ! \ (we have not included cerebellum fully in the slices: is this a problem?) Thanks for your help
On 08/07/2010 16:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
well that certainly looks wrong. What does the original image look like? On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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.
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Hi Lena,
no, not at this time. Sorry.
Bruce On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
Dear Bruce
We are trying to obtain a good contrast in 7T for thickness measurements using freesurfer by piloting different sequences, is there anyway we can process the T2*s in the pipeline?
On 08/07/2010 17:07, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Lena,
-notal-check will disable the error detection, not the tal itself, so won't help in cases where the xform is truly wrong. The image you sent looks PD/T2* weighted, which won't work for the talairaching we use (or for many of our analysis steps).Do you have a T1-weighted image?
cheers Bruce
On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
The original image is attached - Even after notal-check, the recon exits with error mri_watershed Error:
GLOBAL region of the brain empty ! \ (we have not included cerebellum fully in the slices: is this a problem?) Thanks for your help
On 08/07/2010 16:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
well that certainly looks wrong. What does the original image look like? On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached
The error message is
#@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File % tkregister2
Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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.
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Lena Palaniyappan