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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 dbalentine@mgh.harvard.edu
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Balentine, Daniel Grimm DBALENTINE@mgh.harvard.edu 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 dbalentine@mgh.harvard.edu
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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 CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Balentine, Daniel Grimm DBALENTINE@mgh.harvard.edu 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 CautionHello 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?
- Freesurfer version 7.3.0
- 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 dbalentine@mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vyO6jpX8iajK-1t5rnT-drlZOlAx8DRC0xteWXDnkEHJiW...
freesurfer@nmr.mgh.harvard.edu
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Balentine, Daniel Grimm -
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Wighton, Paul