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 -0.180284493 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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