Dear Hedok
Thanks for uploading your data.
The first problem is that your diffusion-weighted images have HIGHER
signal than you non-weighted image. This looks like negative diffusion!!
This could be the result of creating the nifti files with SPM, and
then merging them in FSL. You need to be very careful that SPM does
not scale the data, without updating the scale parameter in the nifti
header, or set the scale parameter without scaling the data..
Do any SPM users know what is done here?
However, even with this, when I run dtifit, I get some output, so
there may also be a problem with your mask.
I ran
avwroi data nodif 0 1
bet nodif nodif_brain -m
dtifit -k data -m nodif_brain_mask -r bvecs -b bvals -m
see if this works
Another couple of points. Is you data matrix 256x256 (1mmx1mm)
native, or did you acquire a smaller matrix, and interpolate to this
number of voxels on the scanne. If the latter, you should try to turn
this interpolation off.
Lastly, 5mm slices are pretty thick if you are thinking about
tractography.
cheers
T
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
[log in to unmask]
www.fmrib.ox.ac.uk/~behrens
On 11 Jul 2006, at 17:37, Hedok Lee wrote:
> Dear FSL experts:
>
> I'm having trouble with "dtifit" (FSL 3.3) as I get blank images after
> running the GUI without having any error. I found two threads
> similar to
> my problems, but I'm not using windows to create "bval" and "bvec"
> files
> so I don't think carriage return is an issue. I'm using Fedora 5.0
>
> I also checked hexcode after each line and I get "ODOA". Do I
> supposed to
> have "OD" only?
>
> These are the threads I found that are similar to my problem.
>
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?
> A2=ind05&L=FSL&D=0&I=-3&P=174618
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=fsl&T=0&P=131083
>
> I'm also attaching output of some commands Tim had suggested in the
> threads, "output of dtifit","bvals", "bvecs", "output of
> bedpost_datacheck", and "output of avwstats". These files are very
> small,
> so I thought it would be ok to attach them.
>
> The binary mask was created by thresholding b0 image at its grand mean
> using SPM5. 4D image was
> created using "avwmerge" over the 26 volumes, where each volume is
> converted from dicom to nifti using SPM5. I checked the 4D image
> using the
> movie feature in "fslview" and looked fine. The order of each
> volume is
> consistent with the "bvec" and "bval" values as well. I also checked
> normalization of diffusion gradients, "bvecs", so that gx2+gy2+gz2=1.
>
> I'm running out of ideas and hope someone can help me with this.
> Please
> let me
> know if you want me to upload the files via FTP.
>
> With regards,
>
> Hedok Lee
> avwstats nodif_brain_mask -r -R -v -V
> 0.000000 1.000000 0.000000 1.000000 1835008 9464063.455748 335274
> 1729177.426508
>
> avwstats ${basename}_FA -r -R -v -V
> 0.000000 0.000000 0.000000 0.000000 1835008 9464063.455748 0 0.000000
>
> avwstats ${basename}_V1 -r -R -v -V
> 0.000000 0.000000 0.000000 0.000000 5505024 28392190.367243 0 0.000000
>
> avwinfo ${basename}_FA
> data_type FLOAT32
> dim1 256
> dim2 256
> dim3 28
> dim4 1
> datatype 16
> pixdim1 1.0156400204
> pixdim2 1.0156204700
> pixdim3 4.9999818802
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
>
> [hel4@localhost FSL_DTI]$ bedpost_datacheck ./
> .//data
> data_type INT16
> dim1 256
> dim2 256
> dim3 28
> dim4 26
> datatype 4
> pixdim1 1.0156400204
> pixdim2 1.0156204700
> pixdim3 4.9999818802
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> .//nodif
> data_type INT16
> dim1 256
> dim2 256
> dim3 28
> dim4 1
> datatype 4
> pixdim1 1.0156400204
> pixdim2 1.0156204700
> pixdim3 4.9999818802
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1
>
> .//nodif_brain_mask
> data_type INT16
> dim1 256
> dim2 256
> dim3 28
> dim4 1
> datatype 4
> pixdim1 1.0156400204
> pixdim2 1.0156204700
> pixdim3 4.9999818802
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1
>
> num lines in .//bvals
> 1
> num words in .//bvals
> 26
> num lines in .//bvecs
> 3
> num words in .//bvecs
> 78
>
>
> 0.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0
> 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0
> 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0 1000.0
>
>
> 0.532212966 0.532212966
> 0.25013984 -0.633506689 -0.218922463 -0.413149806 0.734236034
> 0.936469941 -0.333112408 0.103315488 -0.926539656
> 0.801488967 -0.916836769 -0.537755795 -0.213559058 -0.12413861
> 0.273979937 -0.44331549 0.024170842 0.56836516
> 0.93093039 -0.825458836 0.47259788 0.50426336 0.149335563 -0.69471741
> 0.104012541 0.104012541 -0.721834059 -0.753135633
> 0.850392517 -0.780294228 -0.661803691
> 0.054189066 -0.242859002 -0.991677013 0.372983071
> 0.543143312 -0.261947686 0.438027927 -0.664684481 -0.051815651
> 0.960273113 0.878048334 0.368771526
> 0.637098309 -0.168157727 -0.182178469 -0.629557481 -0.129264527
> 0.68874259 0.344411933
> -0.840196852 -0.840196852 0.645279514 -0.177358379 0.478440719
> 0.469519068 0.151371464 0.346536571
> 0.911073888 -0.076828462 -0.049070314 -0.250221458
> 0.30132001 -0.72038201 -0.715951862 -0.990911067 -0.05301455 -0.180284
> 493 0.929205753 0.52064075 -0.324178329 -0.534255291 -0.616691675
> 0.853820324 -0.709459326 0.631465075
>
>
>
> /usr/local/fsl/bin/dtifit --data=/home/hel4/FSL_DTI/data --out=/
> home/hel4/FSL_DTI/dti --mask=/home/hel4/FSL_DTI/nodif_brain_mask --
> bvecs=/home/hel4/FSL_DTI/bvecs --bvals=/home/hel4/FSL_DTI/bvals
> 0 256 0 256 0 28
> 0 slices processed
> 1 slices processed
> 2 slices processed
> 3 slices processed
> 4 slices processed
> 5 slices processed
> 6 slices processed
> 7 slices processed
> 8 slices processed
> 9 slices processed
> 10 slices processed
> 11 slices processed
> 12 slices processed
> 13 slices processed
> 14 slices processed
> 15 slices processed
> 16 slices processed
> 17 slices processed
> 18 slices processed
> 19 slices processed
> 20 slices processed
> 21 slices processed
> 22 slices processed
> 23 slices processed
> 24 slices processed
> 25 slices processed
> 26 slices processed
> 27 slices processed
> Done!
>
>
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