Thanks! That worked great!
Emily
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Wednesday, February 13, 2008 5:19 pm
Subject: Re: [FSL] FLIRT input error?
> Hi,
>
> The error comes from the fact that you have not specified an output
>
> filename.
> It will not fill one in automatically - you have to specify it.
> The length of filename is fine.
> Just use the structural_brain as input, like you are doing now, and
>
> specify
> an output name and all should be well.
>
> All the best,
> Mark
>
>
> On 13 Feb 2008, at 19:08, Emily Stoneham wrote:
>
> > 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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