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Thanks Doug, For your kind detailed replies. This is really great help.
----- Original Message ----- From: "Douglas Greve" dgreve@mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 7, 2018 9:01:01 PM Subject: Re: [Freesurfer] Origin of freesusrfer output
On 8/7/18 1:45 AM, Ritesh Mahajan wrote:
External Email - Use CautionHi Doug,
I checked the link you suggested. What i understood from this is the origin shift(physical co-ordinate of first voxel) is happening due to the rotation of axis to RAS co-ordinate system. To counter rotation origin shift is done, is that correct?
Yes, it rotates it and shifts the center.
My concern is does free-surfer changes the origin, because it has to re-sample the input image(eg: 512*512*166) to output image (256*256*256)? I think free-surfer might be performing some interpolation to do this re-sampling. Is this origin change is done due to re-sampling or due to rotation or because of both ?
yes, it does perform an interpolation (trilinear by default)
I am more interested in knowing whether the origin shift is done because of re-sampling (input image(eg: 512*512*166) to output image (256*256*256))? If yes, how this is encountered ?
The history of FS is that 20 years ago, it was not practical to deal with hires images, so everything was sampled to 1mm3 8bit. It has been hard to get a way from this.
Thanks, Ritesh Mahajan
Thanks, Ritesh Mahajan
----- Original Message ----- From: "Douglas N. Greve" dgreve@mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 6, 2018 9:22:29 PM Subject: Re: [Freesurfer] Origin of freesusrfer output
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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