ok, this may be a bug i've seen before (but did not report to Chris, shame on me)
carefully check that your images were indeed neurological and not only reported as neurological;)
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Buyean Lee [[log in to unmask]]
Gesendet: Donnerstag, 13. August 2009 21:31
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] FIRST (FSL 4.1.4) segmentation error
Yes, they were sagittally acquired.
From: Andreas Bartsch <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, Aug 13, 2009 12:03 pm
Subject: [FSL] AW: [FSL] FIRST (FSL 4.1.4) segmentation error
were your images sagitally acquired time series?
Von: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] im Auftrag von Mark
Jenkinson [[log in to unmask]<mailto:[log in to unmask]>]
Gesendet: Mittwoch, 12. August 2009 01:13
An: [log in to unmask]<mailto:[log in to unmask]>
Betreff: Re: [FSL] FIRST (FSL 4.1.4) segmentation error
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 -
All the best,
On 11 Aug 2009, at 17:02, Buyean Lee wrote:
> 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
> 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
> Thanks again,
> -----Original Message-----
> From: Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>>
> To: [log in to unmask]<mailto:[log in to unmask]>
> Sent: Tue, Aug 11, 2009 5:49 am
> Subject: Re: [FSL] FIRST (FSL 4.1.4) segmentation error
> 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:
> Just download this and copy it into $FSLDIR/bin/ on your
> machine (replacing the old one) and everything should work
> All the best,
> 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 Ri
ght-Putamen - correct
> > 52 Right-Pallidum - correct
> > 53 Right-Hippocampus - wrong
> > 54 Right-Amygdala - wrong
> > 58 Right-Accumbens-area - wrong