Thanks a lot Doug!
Kindly ...
1. What do you mean by intensity normalized?
2. What is the purpose of conforming the inputs to 256^3 1mm3
2. What is the purpose of conforming the inputs to 256^3 1mm3
3. In order to move mask to diffusion space (FA map) or PET space I do the following:
3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256)
3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 )
3.3 I register FA map to T1 image using FLIRT
3.4 I register the mask to T1 using FLIRT
3.5 I use reversed matrix to move the mask to FA map.
The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps?
Bests,
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Wednesday, November 04, 2015 at 3:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all
On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file
> "norm.mgz" ?
norm has been skull stripped and intensity normalized
> 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel
> dimentions are equal while in orig.mgz it is not)?
They should be the same. It might be differnt than rawavg.mgz or your
input data because we "conform" all inputs to 256^3 1mm3
> 3. Is it correct if I convert norm.mgz to "nii" file and use it as a
> "T1" for further processing?
I don't know without knowing more about the "further processing". It is
not a T1 image itself (ie, the voxel intensities are not T1 in msec).
> bests,
> John Anderson
>
>
>
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> Freesurfer mailing list
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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