Hi Doug,
Thanks you very much for your great and detailed answered.
Kindly one more thing:
when I am tring to run recon-all on "001.mgz" (under the folder mri/orig). If the fov is more than 256 ( e.g 320) recon-all failed. I checked the "recon-all.log" file and I found that it failed because the fov is more than 320 and it says that I need to run recon -all with the flag -cw256.
How can the fov affect the segmentation? in other words is it better to run recon-all on a file with fov less than 256 or more than 256 ? what is the difference in the final output?
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
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: Thursday, November 05, 2015 at 9:39 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all
On 11/5/15 8:37 AM, John Anderson wrote:
Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coilsThanks a lot Doug!Kindly ...1. What do you mean by intensity normalized?
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.2. What is the purpose of conforming the inputs to 256^3 1mm3
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.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 FLIRT3.4 I register the mask to T1 using FLIRT3.5 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) 646-1419Sent: 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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
