Hi Adil,
1. dtifit creating empty images:
This could be a problem with your bvals/bvecs files not having a
carriage return at the end. If you are not using one of the latest FSL
distributions, this will have the effect of considering all bvals=0.
You can solve this by either using the latest version of FSL, or
adding a carriage return at the end of these text files.
2. eddy_correct problem:
This may be due to lack of disk space or writing permissions.
eddy_correct creates many temp files. Check that you have enough disk
space and appropriate permissions where the data are, and as Markus
suggested, you could use fslsplit on your data to see if it manages to
create the temp files.
Cheers,
Saad.
On 8 Jan 2010, at 03:33, Adil Javed wrote:
> Hi,
> here's the output you requested for the files.
> thanks so much for your help.
> aj
>
>>
>> Hi!
>>
>>
>>
>> Seems that your eddy correct was a little hungry ;-).
>>
>> What does it say when you do
>>
>> fslhd <your_data_file_before_eddy_correct>.nii.gz
>>
>> fslhd <your_data_file_after_eddy_correct>.nii.gz
>>
>>
>>
>> Best,
>>
>> Markus
>>
>>
>>
>>
>>
>>
>>
>> 2010/1/7 Adil Javed <[log in to unmask]>
>>
>>
>>
>>> Hi,
>>
>>> I am trying to analyze DTI data to get the FA and MD
>> images by running
>>
>>> DTIFIT. After running the DTIFIT I do get FA,
>> MD, etc images but when I
>>
>>> look at them in FSL view, all these images have
>> intensities of 0. There are
>>
>>> no images to look at. I even played around with
>> min/max itensity from 0-1 or
>>
>>> -1 to 1 and again nothing. I've tried other
>> programs to analyze the same
>>
>>> data, such as DTI tool in MedINRIA, and it works fine
>> there.
>>
>>>
>>
>>>
>>
>>>
>>
>>> also after I run Eddy current correction, the
>> generated file has only 1
>>
>>> volume which looks like b0 file and the remaining 32
>> volumes of various
>>
>>> directions are gone?
>>
>>>
>>
>>> any ideas?
>>
>>>
>>
>>> Thanks for your help,
>>
>>>
>>
>>> aj
>>
>>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>>
>>
>>
>>
>> Dr. med. Markus Gschwind, M.D.
>>
>> Laboratory for Neurology and Imaging of Cognition - Dept of
>> Neurosciences
>>
>> University Medical Center (CMU)
>>
>> 1, Michel-Servet
>>
>> CH-1211 GENEVA - Switzerland
>>
>>
>>
>> Tel 0041 (0) 22 379 5324
>>
>> Fax 0041 (0) 22 379 5402
>>
>> email: [log in to unmask]
>>
>> http://labnic.unige..ch
>>
>>
>>
>>
>>
>>
>>
>>
>> This email is intended only for the use of the individual
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> <DTIFIT problems.odt>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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