Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data?
Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
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
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.
I would not just reverse the images. If something is going wrong with bbregister/mri_vol2vol then it should be fixed. If you don't keep careful track of these things and know exactly what is happening, then it will certainly come back to bite you (or me!). doug
On 12/18/12 11:26 PM, MCLAREN, Donald wrote:
Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data?
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
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
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
When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.htm...
On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald mclaren.donald@gmail.com wrote:
Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data?
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
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
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.
Oh, right, that can be a problem. In 5.2, I've changed it to use nii by default. This breaks when spm2 is used, but then the user can spec to use img instead. doug
On 12/19/12 5:38 PM, MCLAREN, Donald wrote:
When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.htm...
On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald mclaren.donald@gmail.com wrote:
Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data?
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated.
The contents of register.dat are as follows: FS_D011 3.000000 3.540000 0.150000 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
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
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
MCLAREN, Donald