Re: [Freesurfer] apply an existing linear transform to a GRE phase map

[Douglas N. Greve]

External Email - Use Caution

what do you mean that you won't want to do any resampling? How else 
would you apply a transform? Or do you mean that you want to use nearest 
neighbor resampling (so no interpolation)? If so, you can use 
mri_vol2vol with the --interp nearest option

On 5/3/2023 4:21 PM, Wighton, Paul wrote:
>  External Email - Use Caution
>
> Hi Daniel,
>
> It's been a while since I looked into this, but I think you'll need to use 
> `lta_convert` to convert your lta to xfm format, then use 
> `mri_add_xform_to_header` to overwrite the header of your phase map.
>
> You might have to extract the current transform from your phase map, apply 
> the robust_regsiter transformation then write the resulting xfm back to your 
> phase map file.
>
> There is also mri_convert which has an `--apply_transform` flag, but I think 
> that resamples the data.
>
> -Paul
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Balentine, Daniel Grimm 
> 
> Sent: Wednesday, May 3, 2023 4:06 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] apply an existing linear transform to a GRE phase map
>
>  External Email - Use Caution
> Hello FreeSurfer Developers,
>
> I hope you are well. I’m attempting to apply an .lta file generated by 
> mri_robust register. The files I want to apply the transform on are GRE phase 
> maps, so I don’t want to do any resampling.
>
> I was looking around mri_vol2vol, but all the examples seem to involve 
> resampling to a target scan. How would I go about this if I simple want to 
> apply this linear transform on the phase maps (nii) in freesurfer?
>
>
>1.  Freesurfer version 7.3.0
>2.  Platform: CentOS Version 7
>
> Sincerely,
>
> Daniel Balentine
>
> Data Analyst
> Athinoula A Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 - 13th Street
> Charlestown, MA 02129
> dbalent...@mgh.harvard.edu
>
>
>
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Re: [Freesurfer] apply an existing linear transform to a GRE phase map

[Wighton, Paul]

External Email - Use Caution

Hi Daniel,

It's been a while since I looked into this, but I think you'll need to use 
`lta_convert` to convert your lta to xfm format, then use 
`mri_add_xform_to_header` to overwrite the header of your phase map.

You might have to extract the current transform from your phase map, apply the 
robust_regsiter transformation then write the resulting xfm back to your phase 
map file.

There is also mri_convert which has an `--apply_transform` flag, but I think 
that resamples the data.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Balentine, Daniel Grimm 

Sent: Wednesday, May 3, 2023 4:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] apply an existing linear transform to a GRE phase map

External Email - Use Caution
Hello FreeSurfer Developers,

I hope you are well. I’m attempting to apply an .lta file generated by 
mri_robust register. The files I want to apply the transform on are GRE phase 
maps, so I don’t want to do any resampling.

I was looking around mri_vol2vol, but all the examples seem to involve 
resampling to a target scan. How would I go about this if I simple want to 
apply this linear transform on the phase maps (nii) in freesurfer?


  1.  Freesurfer version 7.3.0
  2.  Platform: CentOS Version 7

Sincerely,

Daniel Balentine

Data Analyst
Athinoula A Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 - 13th Street
Charlestown, MA 02129
dbalent...@mgh.harvard.edu



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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.