On 11/5/15 8:37 AM, John Anderson wrote:
Thanks a lot Doug!
Kindly ...
1. What do you mean by intensity normalized?
Removing non-biological intensity fluctuations such as
darkening/brightening from multiple head coils
2. What is the purpose of conforming the inputs to 256^3 1mm3
This is something that was done when FS was first programmed to make it
easier to program by assuring that all inputs were the same size.
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.
Probably works, but very compilcated. You should use bbregister to
register the FA or PET directly to the conformed space, then use
mri_label2vol to map the mask into FA/PET space.
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
*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
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
> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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