Thanks for the explanation, Bruce! Best Regards, Yi
On 13 Nov 2017, at 5:48 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Yi yes, brainmask.mgz is the skull stripped image. And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it) cheers Bruce > On Mon, 13 Nov 2017, Yi Li wrote: > > Hi Bruce, > > Thanks for the help! Is the skull-stripped image in Brainmask.mgz? > > Another question: since my raw image has gone through B1 correction and N3 > normalization, will you suggest I omit the nu and normalize step in > -autorecon1? > > Best Regards, > Yi > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Monday, November 13, 2017 10:50 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [strip skull for unregistered images] > > Hi Yi > > autorecon1 should do the skull stripping, so there is no need for the > separate mri_mask call. The threshold of '5' is so to preserve edits in which > voxels are turned 'off' (they are set to 1 I believe, but we reserve > 2-4 as additional 'off' values). > > The masking will not transform the voxel coordinates of the image > > cheers > Bruce > > >> On Mon, 13 Nov 2017, Yi Li wrote: >> >> >> Dear FS experts, >> >> >> >> I would like to strip skulls from unregistered images which have gone >> through GradWarp, B1-correction, N3 normalization and phantom-based scaling. >> I run the following two commands in freeSurfer: >> >> recon-all -autorecon1 -subjid <subjid> >> >> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz >> >> >> >> My questions are >> >> 1) Currently I use 5 as threshold (-T 5). Is there a guidance for >> the setting of this parameter? >> >> 2) In the output file T1.final.mgz, is the skull-stripped image >> represented in ijk space (image index space) or in XYZ space (via >> transformation matrix)? >> >> 3) If the skull-stripped image is represented in XYZ space, how >> do I get it in ijk space? >> >> >> >> Thanks in advance for the help! >> >> >> >> Best Regards, >> >> Yi Li (PhD) >> >> Senior Computational Scientist >> >> Computational Sciences >> >> The Jackson Laboratory >> >> Farmington, CT 06032 >> >> Tel: 860-837-2156 >> >> >> >> --- >> >> The information in this email, including attachments, may be >> confidential and is intended solely for the addressee(s). If you >> believe you received this email by mistake, please notify the sender >> by return email as soon as possible. >> > --- > > The information in this email, including attachments, may be confidential and > is intended solely for the addressee(s). If you believe you received this > email by mistake, please notify the sender by return email as soon as > possible. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
