also, check out this web page http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 08/05/2018 11:23 AM, Bruce Fischl wrote: > Hi Ritesh > > you can use the vox2ras matrix to compute the RAS coordinates of any > voxel. Just give it column,row,slice,1 indices as the input vector. > > cheers > Bruce > On Sun, 5 Aug 2018, Ritesh Mahajan wrote: > >> 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 >> >> >> > > > _______________________________________________ > 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
