Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

2017-02-03 Thread Douglas Merkitch 
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 
> 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 
> 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_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
>
 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_merki...@rush.edu
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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

2017-02-01 Thread Lilla Zollei 


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  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_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
 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_merki...@rush.edu

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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

2017-01-31 Thread Douglas Merkitch 
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 
> 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_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
>
 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_merki...@rush.edu
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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

2017-01-26 Thread Douglas Merkitch 
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_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
>
 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_merki...@rush.edu
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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

2017-01-26 Thread Lilla Zollei 


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_merki...@rush.edu






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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

2017-01-25 Thread Douglas Merkitch 
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_merki...@rush.edu





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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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