Hi Saad and Markus,
I think u guys figured it out. I don't have a problem with getting Eddy corr_data anymore, with more memory and swap space.
I think as u suggested the reason why my FA, MD, images are intensity of 0 is b/c of my bval file, which all have a value of 0 (see the file). My bvec file looks ok to me (see attached). Not sure why the scanner generated this bval file with all zeros. The other program I use MedINRIA only requires bvec file to draw FA/MD etc maps--so I guess that's why it takes my data. BUT I rather use FSL.
Is there any way to correct my bval file? Is this a scanner thing?
again, many thanks,
adil
--- On Fri, 1/8/10, Saad Jbabdi <[log in to unmask]> wrote:
> From: Saad Jbabdi <[log in to unmask]>
> Subject: Re: [FSL] DTIFIT problems-please help
> To: [log in to unmask]
> Date: Friday, January 8, 2010, 3:56 AM
> 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
> >> or entity to which it is addressed and may
> contain
> >> information that is privileged and confidential.
> If the
> >> reader of this email message is not the intended
> recipient,
> >> you are hereby notified that any dissemination,
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> >> prohibited. If you have received this email in
> error, please
> >> notify the sender and destroy/delete all copies of
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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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