Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3?
Cheers,
Corinna
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii
doug
On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using
the registration from step 3?
Cheers,
Corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered.
4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii
doug
On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using the
registration from step 3?
Cheers,
Corinna
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg ... doug
On 10/15/14 10:19 AM, Corinna Bauer wrote:
Hi Doug,
I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following:
- mni152reg --s MAE_06072013
- tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered.
- mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii doug On 10/14/14 2:57 PM, Corinna Bauer wrote:Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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I'm pretty sure it came from mni152reg. Here are the last few lines of the mni152 reg output:
Final tkRAS-to-tkRAS Matrix is: 1.013 0.045 0.047 -1.659; 0.062 -0.209 -1.043 -15.101; -0.025 0.933 -0.227 33.122; 0.000 0.000 0.000 1.000;
Vox2Vox Matrix is: 2.025 0.094 -0.090 36.461; -0.049 -0.455 -1.865 206.757; -0.124 2.086 -0.418 23.848; 0.000 0.000 0.000 1.000;
Resampling Output registration matrix is identity INFO: writing registration to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.lta transformed matrix: 1.000 0.000 -0.000 -1.566; -0.000 -0.000 -1.000 -23.577; 0.000 1.000 -0.000 9.029; 0.000 0.000 0.000 1.000; transformed matrix: 0.500 0.000 0.000 -18.500; 0.000 0.500 0.000 -9.500; 0.000 0.000 0.500 -18.500; 0.000 0.000 0.000 1.000; INFO: writing registration matrix to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg To check registration, run:
tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
mri_vol2vol done
On Wed, Oct 15, 2014 at 10:28 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg ... doug
On 10/15/14 10:19 AM, Corinna Bauer wrote:
Hi Doug,
I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following:
- mni152reg --s MAE_06072013
- tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered.
- mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii
doug
On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all,I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using the
registration from step 3?
Cheers,
Corinna
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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.
Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space: mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}.
mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
Corinna
On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer corinnab83@gmail.com wrote:
Hi Doug,
I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following:
- mni152reg --s MAE_06072013
- tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered.
- mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii
doug
On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using the
registration from step 3?
Cheers,
Corinna
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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'm not sure what is in that file. Try doing it the way that I suggested and see if it works. doug
On 10/15/14 10:29 AM, Corinna Bauer wrote:
Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space: mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}.
mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
Corinna
On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hi Doug, I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf Up until this point, everything looks good and well registered. 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat Corinna On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii doug On 10/14/14 2:57 PM, Corinna Bauer wrote:Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
I tried your suggestion first and the registration was off, whereby the axial and coronal were switched and sagittal was rotated 90 degrees.
Corinna
On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I'm not sure what is in that file. Try doing it the way that I suggested and see if it works. doug
On 10/15/14 10:29 AM, Corinna Bauer wrote:
Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space: mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}.
mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
Corinna
On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer corinnab83@gmail.com wrote:
Hi Doug,
I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following:
- mni152reg --s MAE_06072013
- tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered.
- mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii
doug
On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all,I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using the
registration from step 3?
Cheers,
Corinna
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
Sorry, I gave you a bad command line. Try this
mri_matrix_multiply -im MAE_06072013/register.dat -iim MAE_06072013/mri/mni152.orig.mgz.reg -om MAE_06072013/newmnireg.dat
doug
On 10/15/2014 10:33 AM, Corinna Bauer wrote:
I tried your suggestion first and the registration was off, whereby the axial and coronal were switched and sagittal was rotated 90 degrees.
Corinna
On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what is in that file. Try doing it the way that I suggested and see if it works. doug On 10/15/14 10:29 AM, Corinna Bauer wrote:Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space: mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat Corinna On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote: Hi Doug, I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf Up until this point, everything looks good and well registered. 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat Corinna On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii doug On 10/14/14 2:57 PM, Corinna Bauer wrote:Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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Hi Doug, That still gives sag rotated -90 degrees, axial shows up as a coronal rotated 180 deg, and coronal shows up as axial.
Corinna
On Wed, Oct 15, 2014 at 11:17 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Sorry, I gave you a bad command line. Try this
mri_matrix_multiply -im MAE_06072013/register.dat -iim MAE_06072013/mri/mni152.orig.mgz.reg -om MAE_06072013/newmnireg.dat
doug
On 10/15/2014 10:33 AM, Corinna Bauer wrote:
I tried your suggestion first and the registration was off, whereby the axial and coronal were switched and sagittal was rotated 90 degrees.
Corinna
On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what is in that file. Try doing it the way that I suggested and see if it works. doug On 10/15/14 10:29 AM, Corinna Bauer wrote:Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space: mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat Corinna On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote: Hi Doug, I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
--targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf Up until this point, everything looks good and well registered. 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat Corinna On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat Check tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii doug On 10/14/14 2:57 PM, Corinna Bauer wrote:Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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