In my experience, dcm2nii gets it right. It would not be okay to assume
that all other bvalues were 1000 if they in fact weren't, but this is fairly
uncommon and dcm2nii wouldn't say they were all 1000 if they were not.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Adil Javed
Sent: Saturday, January 09, 2010 1:44 PM
To: [log in to unmask]
Subject: Re: [FSL] DTIFIT problems-please help
Hi Matt,
after editing my bval file to 0, 1000, 1000, etc. to n directions and then
runing DTIFIT, it seems to work fine. This is acyually what dcm2nii in the
MRICron package did using that coverting sofetware instead of all 0s as was
done by MRIConvert. I guess the other program MedINRIA assumes all b values
other than reference to be 1000.
The question: is this ok?? to assume b values other than reference to be
0.
Many thanks for al those who helped me, Saad, Markus, and you.
adil
--- On Fri, 1/8/10, Matt Glasser <[log in to unmask]> wrote:
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: [FSL] DTIFIT problems-please help
> To: [log in to unmask]
> Date: Friday, January 8, 2010, 10:10 PM
> 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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