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I had to send it again with different Subject because it was rejected before.

-----Original Message-----
From: Buyean Lee <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, 29 Jan 2009 1:22 pm
Subject: Re: [FSL] Can't use FSL FIRST with a Nifti file converted from DICOM with SPM5

The Nifti image converted with SPM5 'DICOM import' was not successfully processed by FSL FIRST (specifically, first_flirt).
The Nifti image converted with dcm2nii was successfully processed  with FSL FIRST.

Caution: I didn't test if this is a generalized problem with 'DICOM import' of SPM5. 

Buyean

-----Original Message-----
From: Mark Jenkinson <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, 29 Jan 2009 9:27 am
Subject: Re: [FSL] Can't use FSL FIRST with a Nifti file converted from DICOM with SPM5

Hi, 
 
Out of interest what was the difference between the two images? 
Do they look different in fslview? 
And can you send the output of fslhd run on the one which worked 
and the one which didn't. 
 
Thanks, 
  Mark 
 
Buyean Lee wrote: 
> I found that dcm2nii solved my problem, although I didn't try MRIconvert. 
> 
> Thank you, 
> 
> Buyean 
> 
> 
> -----Original Message----- 
> From: Benny Liberg <[log in to unmask]> 
> To: [log in to unmask] 
> Sent: Wed, 28 Jan 2009 12:16 am 
> Subject: Re: [FSL] Can't use FSL FIRST with a Nifti file converted > from DICOM with SPM5 
> 
> Try converting your images with MRIconvert 
> 
> Cheers 
> Benny 
> 
> 2009/1/28 Buyean Lee <[log in to unmask] <mailto:[log in to unmask]>> 
> 
> Dear FSL users, 
> 
> I have been successfully using FSL FIRST with T1 MRIs in Analyze 
> file format (I changed origin to AC, the MRI is in MNI 
> orientation, and the neck was cropped). 
> 
> But, when I used FSL FIRST with MRIs in Nifti file format (I used 
> SPM5 DICOM import function to convert DICOM to Nifti), the first 
> step (FIRST_FLIRT) failed. The registered image is totally 
> wrong. Since MRI was acquired in Sagittal plane, I changed the 
> orientation to MNI orientation with fslswapdim. But, the 
> registration is still bad. Cropping neck doesn't help. 
> 
> Since the two key words (First and Nifti) are so common, it is not 
> easy to find any relevant information to this problem. 
> 
> I appreciate any suggestion. 
> 
> Thank you, 
> 
> Buyean > 
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> 
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