Re: [Freesurfer] Origin of freesusrfer output

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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....

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:

...

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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

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