Hi,
Any NaNs in any image are a big problem in FSL
and will cause things to stop working.
You should remove them by running:
fslmaths imagename -nan imagename
which will replace all the NaNs with zeros.
Once you've done this everything should be fine.
All the best,
Mark
On 24 Nov 2009, at 15:01, www wrote:
> Hi Steve,
> The mat file was wrong, it was just nan. Could this be caused by
> a "nan" in the functional images? T1 was just skull stripped using
> bet, but functional images were prefiltered using spm and then
> combined using fslmerge.
>
> Thanks.
>
> Ze
>
> --- On Tue, 11/24/09, Stephen Smith <[log in to unmask]> wrote:
>
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: [FSL] registration error
> To: [log in to unmask]
> Date: Tuesday, November 24, 2009, 12:16 PM
>
> Hi - can you try
>
> cd <your ICA output directory>
> cd reg
> ls -lrt
>
> and then run the first flirt command below and see what happens?
> This flirt failed, which is unusual; probably either there's
> something wrong in the input data or maybe the image was too large
> for the RAM/swap that your computer has.
>
> Cheers.
>
>
> On 24 Nov 2009, at 03:47, www wrote:
>
>> Dear all,
>> This time, I set up MELODIC to run ica for just one subject,
>> and I get another registration problem. I didn't select any
>> preprocessing for the functional 4D data (no motion correction, no
>> highpass low pass filtering). I have selected the high res T1 as
>> the main structure image for registration. The settings are
>> default. The error message is attached below. Could somebody point
>> out what is the problem? This is the first time I'm trying FSL.
>>
>> Many thanks!
>>
>> Ze
>>
>> /bin/mkdir -p reg
>>
>> /usr/local/fsl/bin/fslmaths /jet/zwang/testretest/FSLICA/
>> sub10_T1_sub10 highres
>>
>> /usr/local/fsl/bin/fslmaths /usr/local/fsl-4.1.0_32bit/data/
>> standard/MNI152_T1_2mm_brain standard
>>
>> /usr/local/fsl/bin/flirt -ref highres -in example_func -out
>> example_func2highres -omat example_func2highres.mat -cost corratio -
>> dof
>> 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp
>> trilinear
>>
>> /usr/local/fsl/bin/convert_xfm -inverse -omat
>> highres2example_func.mat example_func2highres.mat
>> Cannot read input-matrix
>>
>> /usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35
>> sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
>> sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
>> sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/
>> local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png +
>> sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png
>> + sll.png example_func2highres1.png ; /usr/local/fsl/bin/slicer
>> highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -
>> x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
>> 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z
>> 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png
>> + slb.png + slc.png + sld.png +
>> sle.png + slf.png + slg.png + slh.png + sli.png + slj.png +
>> slk.png + sll.png example_func2highres2.png ; /usr/local/fsl/bin/
>> pngappend example_func2highres1.png - example_func2highres2.png
>> example_func2highres.png; /bin/rm -f sl?.png
>> WARNING: input image is empty
>>
>> /usr/local/fsl/bin/flirt -ref standard -in highres -out
>> highres2standard -omat highres2standard.mat -cost corratio -dof 12
>> -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>>
>> /usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat
>> highres2standard.mat
>>
>> /usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35
>> sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
>> sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
>> sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/
>> local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png +
>> sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png +
>> sll.png highres2standard1.png ; /usr/local/fsl/bin/slicer standard
>> highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55
>> slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55
>> slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
>> slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
>> slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png
>> + sli.png
>> + slj.png + slk.png + sll.png highres2standard2.png ; /usr/local/
>> fsl/bin/pngappend highres2standard1.png - highres2standard2.png
>> highres2standard.png; /bin/rm -f sl?.png
>>
>> /usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -
>> concat highres2standard.mat example_func2highres.mat
>> Cannot read input-matrix
>>
>> /usr/local/fsl/bin/flirt -ref standard -in example_func -out
>> example_func2standard -applyxfm -init example_func2standard.mat -
>> interp trilinear
>> Could not open matrix file example_func2standard.mat
>>
>> /usr/local/fsl/bin/convert_xfm
>> -inverse -omat standard2example_func.mat example_func2standard.mat
>> Could not open matrix file example_func2standard.mat
>> Cannot read input-matrix
>>
>> /usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x
>> 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y
>> 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z
>> 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png
>> -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png +
>> slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png
>> + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/
>> local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35
>> sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
>> sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
>> sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/
>> local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png +
>> sle.png + slf.png + slg.png + slh.png + sli.png +
>> slj.png + slk.png + sll.png example_func2standard2.png ; /usr/
>> local/fsl/bin/pngappend example_func2standard1.png -
>> example_func2standard2.png example_func2standard.png; /bin/rm -f
>> sl?.png
>> ** ERROR (nifti_image_read): failed to find header file for
>> 'example_func2standard'
>> ** ERROR: nifti_image_open(example_func2standard): bad header info
>> Error: failed to open file
>> example_func2standard
>> ERROR: Could not open image example_func2standard
>> Image Exception : #22 :: Failed to read volume example_func2standard
>> terminate called after throwing an instance of
>> 'RBD_COMMON::BaseException'
>> sh: line 1: 9271 Aborted /usr/local/fsl/bin/slicer
>> example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png
>> -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
>> 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z
>> 0.55 slk.png -z 0.65 sll.png
>>
>>
>>
>> --- On Tue, 11/24/09, Alexander Lebedev <[log in to unmask]> wrote:
>>
>> From: Alexander Lebedev <[log in to unmask]>
>> Subject: [FSL] Asymmetrical design
>> To: [log in to unmask]
>> Date: Tuesday, November 24, 2009, 3:52 AM
>>
>> Dear FSL users,
>>
>> Sorry for stupid question... Is it possible to estimate an
>> asymmetrical design (with different number of subjects in three
>> groups: 12 controls, 27 and 8 patients)?
>>
>> Best Regards,
>> Alexander Lebedev
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
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