Dear Bruce,

thank you for your fast reply ,I think I could not explain the problem correctly . I want the number of slices in aseg file convert from 256x256x256 to 208x176x176(the subject size) so I can enable to compute the dice coefficient with my Matlab code ? any suggestions how can I make it possible?

Best Regards, Nazanin

On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Nazanin

all our segmentations are in subject space, so it should be pretty straightforward

cheers Bruce

On Mon, 9 Jan 2017, N Saf wrote:

Dear freesurfers,

...

I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have manual segmentation for hippocampus in my subject space(208x176x176)as well. I want to compute the dice coefficient with one simple Matlab code. how can I do it correctly ?if I want to bring the aseg to subject space , which command with which options is the best way to do it correctly ?any help can be appreciated.(I did it for the FSL segmentation result but it was simple because the result is in my subject space).

Best Regards, Nazanin

---

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Dear Bruce,

Thank you very much,you are a life saver..

Best, Nazanin

On Mon, Jan 9, 2017 at 11:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

yes, you can use mri_convert as follows:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

assuming the rawavg.mgz has the 208x176x176 dimensions (which it should)

cheers Bruce On Mon, 9 Jan 2017, N Saf wrote:

Dear Bruce,

...

thank you for your fast reply ,I think I could not explain the problem correctly . I want the number of slices in aseg file convert from 256x256x256 to 208x176x176(the subject size) so I can enable to compute the dice coefficient with my Matlab code ? any suggestions how can I make it possible?

Best Regards, Nazanin

On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nazanin

  all our segmentations are in subject space, so it should be pretty

straightforward

  cheers
  Bruce
  On Mon, 9 Jan 2017, N Saf wrote:

        Dear freesurfers,

        I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256)

and I have manual segmentation for hippocampus in my subject space(208x176x176)as well. I want to compute the dice coefficient with one simple Matlab code. how can I do it correctly ?if I want to bring the aseg to subject space , which command with which options is the best way to do it correctly ?any help can be appreciated.(I did it for the FSL segmentation result but it was simple because the result is in my subject space).

        Best Regards,
        Nazanin

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 http://www.partners.org/complianceline . 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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 http://www.partners.org/complianceline . 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.