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:
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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" dgreve@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....
- 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:
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Hi Bruce,
- 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
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