Dear Mark and all,
I followed you steps and tried to use eddy_correct in the last
several days.
Actually I made 4D volumes with different software and methods, but
every time I got the same error message as follows. Would you please
tell me the reason?
I am eager to see the results of eddy current correction asap.
Thank you very much.
=================================
in the following command line, mergeout_a.hdr and mergeout_a.img is a
pair representing a 4d volume
===================================
hippo:/usr/local/fsl/bin> eddy_correct /home/cuij/3D/mergeout_a.hdr
/hippo_SAN/jiali/temp/out 1
Error: failed to open file vol0000.img
Error:: FslCloneHeader: Null pointer passed for FSLIO
Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
vol*: No such file or directory
=====================================
Best Wishes
Jiali Cui
>>> Mark Jenkinson <[log in to unmask]> 02/15/07 4:33 PM >>>
Hi,
You can try mri_convert from the FreeSurfer package for getting
dicom images into nifti format, or look at the link on our FAQ at:
http://www.fmrib.ox.ac.uk/fslfaq/#general_format
You may also need to you avwmerge to concatenate 2D or 3D
images into 4D images, depending on the conversion tool you
choose. This is also detailed on our FAQ.
All the best,
Mark
On 15 Feb 2007, at 21:10, Jiali Cui wrote:
> Dear Mark and all,
>
> Thanks again for your keeping me informed. Now I want to know
how
> to prepare input 4D image.
>
> I tried in the last hours and failed to get a result.
>
> As you know the command line of eddy current correction is as
> follows.
>
> eddy_correct <4dinput> <4doutput> <reference_no>
>
> But I met troubles in preparing 2D input images. Does anyone
know
> how to convert a series of dicom images to 4D images which FSL
> required?
> Is there a file which introduce in detail the usage of
eddy_correct?
>
> Thanks.
>
> All the best.
>
> J.
>
>
>
>
>>>> Mark Jenkinson <[log in to unmask]> 02/13/07 4:53 PM >>>
> Dear Jiali,
>
> There is a tool called eddy_correct which you can run
> either from the command line or from the FDT gui.
> I recommend you use that.
>
> All the best,
> Mark
>
>
> On 13 Feb 2007, at 21:04, Jiali Cui wrote:
>
>> Hi, everyone,
>>
>> Actually, I mainly want to known the usage of flirt when it is
>> applied to eddy current correction.
>>
>> Thank you very much.
>>
>> Best
>> J.
>>
>>
>>>>> Jiali Cui <[log in to unmask]> 02/13/07 12:23 PM >>>
>> Hi, everyone,
>>
>> I have THREE questions about FSL flirt. Would some guy can help
> me
>> with this? Thanks.
>>
>> (1) I found negative values in the results when I use FSL
> flirt.
>> Does anyone know why?
>>
>> My experiments includes the following steps.
>>
>> First, I use the flirt package to do image coregistration.
>> the
>> command line is shown as follows.
>>
>> flirt -in inslice.hdr -ref refslice.hdr -out outslice
> -omat
>> omat.txt -2D
>>
>> Then I used NII package to see the results named
>> outslice.nii,
>> and found negative values. Why?
>>
>> (2) How to use flirt to correct distortion induced by eddy
> current?
>>
>> (3) Is there any good tools to read and write nii format images?
>>
>> Thanks a lot.
>>
>> J.
>>
>> Best Wishes
>>
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