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....
- Yes, unless you tell recon-all not to.
- 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 CautionHi Bruce,
- Free-surfer output is always 256*256*256, regardless of any input dimensions.
- I have a doubt, while doing this re-sampling from input dimension to 256*256*256. Does free-surfer change the origin of image?
- My input is an MRI dicom image, for dicom tag value (0020,0032) which gives me the image position(origin).
- 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