Ask whoever runs your scanner what bvalue was used. You might also be able
to find out the information yourself from the DICOM header. Also, you might
try dcm2nii in the MRICron package and see if that gives you a correct bvals
file. Not sure how the other program works without knowledge of the bvalue,
perhaps you set it somewhere in the program or it just assumes 1000?
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Adil Javed
Sent: Friday, January 08, 2010 9:53 PM
To: [log in to unmask]
Subject: Re: [FSL] DTIFIT problems-please help
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,
> >> distribution, or copying of this communication is
> >> prohibited. If you have received this email in
> error, please
> >> notify the sender and destroy/delete all copies of
> the
> >> transmittal. Thank you.
> >>
> > <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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