External Email - Use Caution Thanks Bruce.
Thanks Doug for clearing this. Can you please tell, how can i get back the first voxel of input ? Also, can you tell what mathematical formula or equation is used convert this origin ? Thanks, Ritesh Mahajan ----- Original Message ----- From: "Douglas Greve" <dgr...@mgh.harvard.edu> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, August 3, 2018 9:51:30 PM Subject: Re: [Freesurfer] Origin of freesusrfer output To add on, the origin is changed in that the "first voxel" is not the same in the 256^3 volume as it is in the original dicom. Having said that, all our files (eg, mgz and nifti) have a matrix that converts a col, row, slice into the scanner RAS, so you can always find your way back to the dicom coordinates. On 8/3/18 10:41 AM, Bruce Fischl wrote: > Hi Ritesh > > Doug can correct any inaccuracies, but.... > > 1. Yes, unless you tell recon-all not to. > 2. I'm not sure what you mean by the origin, but we do keep track of > the ras coordinates of the center of the volume after resampling (the > so-called "cras"). > 3. We do keep track of the original dicom coordinates. > 4. mri_info will spit out various matrices, among them the voxel to ras > transform that should take you back to scanner ras coordinates. > > cheers > Bruce > > On Fri, 3 Aug 2018, Ritesh > Mahajan wrote: > >> External Email - Use Caution >> >> Hi Bruce, >> >> 1) Free-surfer output is always 256*256*256, regardless of any input >> dimensions. >> 2) I have a doubt, while doing this re-sampling from input dimension to >> 256*256*256. Does free-surfer change the origin of image? >> 3) My input is an MRI dicom image, for dicom tag value (0020,0032) which >> gives me the image position(origin). >> 4) How can i know the origin of free-surfer output in nii format? Do >> free-surfer change this value during processing? >> >> Can you please provide your valuable comments on this. >> >> Thanks, >> Ritesh Mahajan >> >> >> > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
