Hi Bruce, Thank you for the message. My image has isotropic voxel size 1mm3. Is there a way where i can keep the original matrix size (256x256x160) instead of re-sampling to (256x256x256)? or is there a way where i can resample the data to my original matrix size after i run recon-all?
Thank you. On Mon, Apr 3, 2017 at 5:37 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Dhaval > > we resample all input images to 256^3 and 1mm isootropic unless we are > explicitly told not to. We call this "conforming" > > cheers > Bruce > > On Mon, 3 Apr 2017, Dhaval Shah wrote: > > > Just a correction, > > > > The original image matrix size is (256x256x160) and the resulted image > > matrix size is (256x256x256). > > > > On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah <ds...@bnac.net> wrote: > > Hi All, > > > > I am new and a very basic question about freesurfer processing. > > > > I ran recon-all on a high res-T1 image(128x128x80 matrix size), but > > after recon-all the folder mri contains resulted (brain.mgz and > > orig.mgz) T1 images has (127x128x128 matrix size). > > > > 1) how come the dimensions are changed? Is it normal? > > 2) how can i keep the dimensions same as the original? > > 3) is it possible that i will always get the higher matrix size image > > data? > > > > for simplicity, i converted resulted orig.mgz to nii format and loaded > > it in to fslview. Please find the first image (Original) and the > > second image (after recon-all but orig.mgz). > > > > Your help is greatly appreciated. > > > > -- > > Kind regards, > > Dhaval Shah > > > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > > Buffalo Neuroimaging Analysis Center > > State University of New York at Buffalo > > Department of Neurology > > 100 High St., D-2, Buffalo, NY 14203 > > ds...@bnac.net//http://mbl.bnac.net > > > > > > > > > > -- > > Kind regards, > > Dhaval Shah > > > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > > Buffalo Neuroimaging Analysis Center > > State University of New York at Buffalo > > Department of Neurology > > 100 High St., D-2, Buffalo, NY 14203 > > ds...@bnac.net//http://mbl.bnac.net > > > > > _______________________________________________ > 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. > > -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203ds...@bnac.net//http://mbl.bnac.net
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