Hello Freesurfer experts,
From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other steps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid.
Lilla
On Wed, 25 Jan 2017, Douglas Merkitch wrote:
Hello Freesurfer experts, From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edu
Hello Lilla,
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks for your help!
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Jan 26, 2017, at 8:42 AM, Lilla Zollei <lzollei@nmr.mgh.harvard.edumailto:lzollei@nmr.mgh.harvard.edu> wrote:
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid.
Lilla
On Wed, 25 Jan 2017, Douglas Merkitch wrote:
Hello Freesurfer experts,
From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Hello,
I'm reposting the following just in case anyone has any ideas. Any input would be greatly appreciated!
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center
On Jan 26, 2017, at 2:41 PM, Douglas Merkitch <Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu> wrote:
Hello Lilla,
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks for your help!
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Jan 26, 2017, at 8:42 AM, Lilla Zollei <lzollei@nmr.mgh.harvard.edumailto:lzollei@nmr.mgh.harvard.edu> wrote:
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid.
Lilla
On Wed, 25 Jan 2017, Douglas Merkitch wrote:
Hello Freesurfer experts,
From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Hi Doug, This seems correct. What do you mean by "not so great"? Could you send files to look at? Lilla
On Tue, 31 Jan 2017, Douglas Merkitch wrote:
Hello, I'm reposting the following just in case anyone has any ideas. Any input would be greatly appreciated!
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center
On Jan 26, 2017, at 2:41 PM, Douglas Merkitch Douglas_Merkitch@rush.edu wrote:
Hello Lilla,Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks for your help!
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edu
On Jan 26, 2017, at 8:42 AM, Lilla Zollei lzollei@nmr.mgh.harvard.edu wrote:
Hi Doug, In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid. Lilla On Wed, 25 Jan 2017, Douglas Merkitch wrote: Hello Freesurfer experts, >From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... KieVE66SX3Ir1tlN37BRLB4VQ1-_CXu_YU&s=DdSn-QyWFHp-MTwopX67ieGs0qeOA8DRaFxeYtykZxM&e=
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Hey Lilla,
I found the error that I made in the original command I posted; I forgot to switch the --targ & --mov inputs in the first mri_vol2vol command. Here's the corrected version that works for me:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $SUBJECTS_DIR/$subj/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Thanks again for the help!
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center
On Jan 31, 2017, at 12:14 PM, Douglas Merkitch <Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu> wrote:
Hello,
I'm reposting the following just in case anyone has any ideas. Any input would be greatly appreciated!
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center
On Jan 26, 2017, at 2:41 PM, Douglas Merkitch <Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu> wrote:
Hello Lilla,
Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --inv-morph \ --mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --o temporary_volume.mgz \ --interp trilin --no-save-reg
mri_vol2vol --targ temporary_volume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do the above commands look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks for your help!
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Jan 26, 2017, at 8:42 AM, Lilla Zollei <lzollei@nmr.mgh.harvard.edumailto:lzollei@nmr.mgh.harvard.edu> wrote:
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid.
Lilla
On Wed, 25 Jan 2017, Douglas Merkitch wrote:
Hello Freesurfer experts,
From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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freesurfer@nmr.mgh.harvard.edu
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Douglas Merkitch -
Lilla Zollei