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Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia
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Dear Rosalia,
I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to get your desired skull stripping. Name the result brainmask.mgz and continue with recon-all –autorecon2 –autorecon3.
Remember that FreeSurfer requires to have the cerebellum attached to the brain. Also inputting the already skull stripped volume in autorecon1 may fail during talairach registration and potentially cause errors during skull stripping (if not skipped anyways).
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta Aguayo Gesendet: Donnerstag, 18. Oktober 2018 06:30 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] autorecon1 with skull stripped image
External Email - Use Caution Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia
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Dear Falk,
Thank you very much for your explanation. One more thing: nii.gz format is also good for FreeSurfer, right?
Best regards, Rosalia
El jue., 18 oct. 2018 8:26, Falk Lüsebrink falk.luesebrink@ovgu.de escribió:
External Email - Use CautionDear Rosalia,
I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to get your desired skull stripping. Name the result brainmask.mgz and continue with recon-all –autorecon2 –autorecon3.
Remember that FreeSurfer requires to have the cerebellum attached to the brain. Also inputting the already skull stripped volume in autorecon1 may fail during talairach registration and potentially cause errors during skull stripping (if not skipped anyways).
Best,
Falk
*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Donnerstag, 18. Oktober 2018 06:30 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] autorecon1 with skull stripped image
External Email - Use Caution *Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull.
Thank you very much for your time,
Rosalia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Rosalina,
yes, it is. FreeSurfer can handle all formats given in the help of mri_convert.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta Aguayo Gesendet: Donnerstag, 18. Oktober 2018 08:48 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] autorecon1 with skull stripped image
External Email - Use Caution Dear Falk,
Thank you very much for your explanation. One more thing: nii.gz format is also good for FreeSurfer, right?
Best regards, Rosalia
El jue., 18 oct. 2018 8:26, Falk Lüsebrink <falk.luesebrink@ovgu.demailto:falk.luesebrink@ovgu.de> escribió:
External Email - Use Caution Dear Rosalia,
I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to get your desired skull stripping. Name the result brainmask.mgz and continue with recon-all –autorecon2 –autorecon3.
Remember that FreeSurfer requires to have the cerebellum attached to the brain. Also inputting the already skull stripped volume in autorecon1 may fail during talairach registration and potentially cause errors during skull stripping (if not skipped anyways).
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta Aguayo Gesendet: Donnerstag, 18. Oktober 2018 06:30 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: [Freesurfer] autorecon1 with skull stripped image
External Email - Use Caution Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Falk Lüsebrink -
Rosalia Dacosta Aguayo