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FSL  August 2009

FSL August 2009

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Subject:

Re: FIRST (FSL 4.1.4) segmentation error

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 12 Aug 2009 00:13:07 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (101 lines)

Hi,

Everything should work fine with either radiological orientation or
neurological orientation.  This recent bug was the only exception
I know about.  So I wouldn't worry - the website warning is not
really necessary anymore, although we internally always use
radiological, so it gets tested a bit more.  However, all the tools
have gone through tests for both neurological and radiological.
This latest problem was just an isolated oversight - sorry.

All the best,
	Mark


On 11 Aug 2009, at 17:02, Buyean Lee wrote:

> 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

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