Hi - I'm not sure what's wrong here - feel free to upload the
complete set of images and bvecs/bvals files for us to check.
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Steve
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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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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