Hi,

Thank you for the fix.
Out of curiosity, I used 'dcm2niigui' (part of Mricron) to convert DICOM to Nifti.
Does this mean that dcm2niigui saves Nifti file in neurological orientation?
I read some emails that recommended dcm2nii in FSL application, but FSL website recommends radiological orientation and warns that some FSL tools will not work correctly when the images are not in radiological orientation (is it still true?).

I wonder how one can convert DICOM to Nifti file in radiological orientation.

Thanks again,


Buyean


 

neurologically-ordered 



-----Original Message-----
From: Mark Jenkinson <[log in to unmask]>
To: [log in to unmask]
Sent: Tue, Aug 11, 2009 5:49 am
Subject: Re: [FSL] FIRST (FSL 4.1.4) segmentation error

Hi, 
 
This turns out to only be a problem for the FAST boundary 
correction method when applied to neurologically-ordered 
images. It is easy to fix in the first_boundary_correction 
script, and the fixed version can be downloaded from: 
  http://www.fmrib.ox.ac.uk/fsldownloads/patches/first_boundary_corr 
 
Just download this and copy it into $FSLDIR/bin/ on your 
machine (replacing the old one) and everything should work 
fine. 
 
All the best, 
  Mark 
 
 
On 11 Aug 2009, at 01:45, Buyean Lee wrote: 
 
> Hi, 

> FSL: version 4.1.4 
> Tool: FIRST. 

> I found that many boundary-corrected ROIs (in > *_all_fast_firstseg.nii) are not registered to the originally > segmented ROIs (in *_all_fast_orisegs.nii); see below for the list. 

> In contrast, the boundary-corrected ROIs generated with an old > version (FSL 4.1.2) are correctly registered to the original ROIs. 

> Let me know where I need to check to fix this error. 

> Thank you, 

> Buyean 

> 4 Left-Lateral-Ventricle - wrong 
> 10 Left-Thalamus-Proper - correct 
> 11 Left-Caudate - wrong 
> 12 Left-Putamen - correct 
> 13 Left-Pallidum - correct 
> 16 Brain-Stem /4th Ventricle – left-right flipped 
> 17 Left-Hip pocampus - wrong 
> 18 Left-Amygdala - wrong 
> 26 Left-Accumbens-area - wrong 
> 43 Right-Lateral-Ventricle - w rong 
> 49 Right-Thalamus-Proper - correct 
> 50 Right-Caudate - wrong 
> 51 Right-Putamen - correct 
> 52 Right-Pallidum - correct 
> 53 Right-Hippocampus - wrong 
> 54 Right-Amygdala - wrong 
> 58 Right-Accumbens-area - wrong