Hi,
1st, thanks so much for helping me out.
So, the corr_data file seems to be fine to me, please see the attached output for fslsplit corr_data.nii.gz. I even see all the 33 volumes in fslview of the corr_data.nii.gz. I got this to work out so far.
But when I run DTIFIT program and get the FA, MD, files, then I see nothing. The intensity is zero. see the attached files. when I run the command fslstats dti_FA.nii.gz -R, I get min/max intensities of 0.000000 0.000000
again, thanks for your time.
aj
--- On Fri, 1/8/10, Markus Gschwind <[log in to unmask]> wrote:
> From: Markus Gschwind <[log in to unmask]>
> Subject: Re: [FSL] DTIFIT problems-please help
> To: FSL@JISCMAIL.AC..UK
> Date: Friday, January 8, 2010, 2:30 AM
> Hi,
>
> It seems everything all right. Both files have the sime
> dimensions:
> dim0 4
> dim1 256
> dim2 256
> dim3 32
> dim4 33
>
> Which means you should find the 33 volumes in both files.
>
>
> How did you find that there was nothing? You can try
> fslsplit corr_data.nii.gz
>
> this will split up the 4D file in its 33 volumes. You can
> have a look at them separately.
> fslstats vol....nii.gz -R
>
> Did you have a look at data.nii.gz? Is it really all
> right?
>
>
> Best,
> Markus
>
>
>
>
>
> 2010/1/8 Adil Javed <[log in to unmask]>
>
> 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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>
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>
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