Re: [Freesurfer] registration and resampling in native space

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Hi Doug,

Could you advise me about how to correctly run mri_vol2vol? The functional data did not get perfectly registered to the anatomy so I'm afraid I'm not running it correctly.

Thanks!

Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl < fischl@nmr.mgh.harvard.edu> ha scritto:

Hi Francesca

sorry, I defer to Doug on the details of mri_vol2vol.

cheers Bruce

On Tue, 12 Feb 2019, Francesca Strappini wrote:

...

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Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o

func_data_registered2T1.nii.gz --no-resample

...

Then I checked the registration and it seems that the original run is

better aligned to the T1 than

...

the registered one. Maybe am I not running mri_vol2vol correctly?

Thanks! Best

Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl <

fischl@nmr.mgh.harvard.edu> ha scritto:

...

  Hi Francesca

  check out the --no-resample option in mri_vol2vol. It just changes

the

...

  header, so I think should do what you want.

  cheers
  Bruce


  On Tue, 12 Feb 2019, Francesca Strappini wrote:

  >
  >         External Email - Use Caution
  >
  > Dear Freesurfer's experts,
  >
  > I would like to register some functional data to the T1, that

were collected in

...

  separate days.
  > I used bbregister:
  >
  > bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat

--init-coreg --t1

...

  >
  > Now, I would like to resample the data based on the register.dat

without upsampling

...

  and keeping the
  > same FoV (3x3x3 mm; 64 64 50). Is it doable?
  >
  > Thanks!
  > Best
  >
  >
  > --
  > Francesca Strappini, Ph.D.
  > Neurobiology Department
  > Weizmann Institute of Science
  > 234 Herzl Street, Rehovot 7610001 Israel
  > Tel.: +972 58 444 2584
  > E-mail: francesca.strappini@weizmann.ac.il
  >
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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il

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