Dear Timothy and all
thank you for your quick response.
And please see below for the results you want. If you need any
other information, please let me know.
================
==============
It's a mystery.
Could you send the outputs of the following commands:
Best Wishes
Jiali Cui
>>>>> avwinfo mergeout_a
hippo:/usr/local/fsl/bin> avwinfo /home/cuij/3D/mergeout_a.hdr
data_type
dim1 256
dim2 256
dim3 51
dim4 14
datatype 16
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
glmax 0
glmin 0
origin1 0
origin2 0
origin3 0
file_type ANALYZE-7.5
>>>>>>>avwstats mergeout_a -R -r
avwstats /home/cuij/3D/mergeout_a.hdr -R -r
0.000000 7621.000000 0.000000 1867.145000
>>>>ls -ld .
drwxr-xr-x 2 root other 5120 Jan 24 14:04 ./
(the current dir is /usr/local/fsl/bin)
also, could you run the following command
>>>> avwsplit mergeout_a
avwsplit /home/cuij/3D/mergeout
Error: failed to open file vol0000.img
Error:: FslCloneHeader: Null pointer passed for FSLIO
(this is the same error message I sent you before)
and send the output of:
>>>> ls -l vol0000.*
ls -l vol0000.*
-rw-r--r-- 1 cuij staff 348 Feb 21 09:05 vol0000.hdr
-rw-r--r-- 1 cuij staff 6684672 Feb 21 09:05 vol0000.img
(the current dir is /home/cuij/3D/)
>>>>>> avwinfo vol0000
avwinfo vol0000
data_type
dim1 256
dim2 256
dim3 51
dim4 1
datatype 4
pixdim1 2.5000000000
pixdim2 2.5000000000
pixdim3 2.5000000000
pixdim4 0.0000000000
cal_max 0.0000
cal_min 0.0000
glmax 0
glmin 0
origin1 0
origin2 0
origin3 0
file_type ANALYZE-7.5
>>>>>>avwstats vol0000 -R -r
avwstats vol0000 -R -r
0.000000 7621.000000 0.000000 2804.528000
==================
================
>>> Tim Behrens <[log in to unmask]> 02/21/07 11:50 AM >>>
It's a mystery.
Could you send the outputs of the following commands:
avwinfo mergeout_a
avwstats mergeout_a -R -r
ls -ld .
also, could you run the following command
avwsplit mergeout_a
and send the output of:
ls -l vol0000.*
avwinfo vol0000
avwstats vol0000 -R -r
Thanks
T
On 21 Feb 2007, at 16:22, Jiali Cui wrote:
> 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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