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FSL  February 2008

FSL February 2008

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Subject:

Re: FLIRT input error?

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Thu, 14 Feb 2008 08:04:33 +0000

Content-Type:

text/plain

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text/plain (79 lines)

Actually both problems in the command line "-out  -omat .mat" are caused
by not specifying an output image name in the GUI.  If you specify an
output image name both problems will be fixed and everything should  
work.

All the best,
	Mark


On 13 Feb 2008, at 23:27, Matt Glasser wrote:

> It looks like you need to specify the name of the transformation  
> matrix that
> is to be output, in addition to the output filename of the transformed
> image.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf
> Of Emily Stoneham
> Sent: Wednesday, February 13, 2008 2:09 PM
> To: [log in to unmask]
> Subject: [FSL] FLIRT input error?
>
> Hello again.  I am new to fMRI and to FSL, so forgive me if this is an
> ignorant question, but in
> FLIRT, (using the feeds data to learn the system) it defaults to a  
> reference
> image of:
> /Users/MLE/fsl/data/standard/MNI152_T1_2mm_brain
>
> What do I put in for an input image?  I assume that I want a  
> structural, so
> I was using
> /Users/MLE/Desktop/FSL/feeds/data/structural_brain.nii.gz
>
> and I assume as well that it should default to some output image?   
> I.e., I
> don't put that in myself?
>
> When I hit 'go', it gives me this error:
>
> /Users/MLE/fsl/bin/flirt -in
> /Users/MLE/Desktop/FSL/feeds/data/structural_brain.nii.gz -ref
> /Users/MLE/fsl/data/standard/MNI152_T1_2mm_brain -out  -omat .mat - 
> bins 256
> -cost corratio
> -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp
> trilinear
> WARNING: change in option usage
>
> To specify the input volume the option -in should be used
> Accepting the filename for now, but please update to new syntax in  
> future.
>
> ** ERROR (nifti_image_read): failed to find header file for '.mat'
> ** ERROR: nifti_image_open(.mat): bad header info
> Error: failed to open file .mat
> ERROR: Could not open image .mat
> Image Exception : #22 :: Failed to read volume .mat
> terminate called after throwing an instance of  
> 'RBD_COMMON::BaseException'
> Finished
>
>
> A) am I using the wrong images?  If so, what images am I to use?
> B) What does this error mean?
> C) could it be that it doesn't like the length of the filename?   
> That it has
> to go too deep for the
> data (through too many folders)?
>
> Thanks!
> Emily
>

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