If you're doing a recon, then there should be an mri/orig.mgz which is conformed (ie, the dimension and voxel size will be 256^3 and 1mm^3) regardless of what you start with. This is what you should be doing all of your operations on (not necessarily orig.mgz, but a conformed volume).

doug

Faden, Eric (NIH/NIMH) [F] wrote: 
So my images come off the scanner as DICOM.

Steps For Both:
1) Convert DICOM to ANALYZE
2) Align and Average the scans

Steps For Broken:
3) Convert to minc to create a brain mask and do some normalization
4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys)
5) Use mri_convert to convert MNC to MGZ

Steps for Working:
3) Convert Analyze to AFNI
4) Use 3drefit (AFNI) to fake 1.0mm voxels
5) Use mri_convert to convert BRIK to MGZ

-Eric

-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Tue 8/1/2006 2:27 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems)
 
can you give us details about how you did the conversion?
On Tue, 1 Aug 
2006, Faden, Eric (NIH/NIMH) [F] wrote:

  
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ.  I have tried the exact same scan going through Analyze to MGZ and the control points work fine.  Has anyone had any issues converting between mnc and mgz?

-Eric

-----Original Message-----
From: Faden, Eric (NIH/NIMH) [F]
Sent: Tue 8/1/2006 9:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Vanishing Control Points

I am currently running 3.0.3 on RedHat EL v4.  Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them.  FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display.  Any ideas why?

-Eric

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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