Hi Hedok - good news!
> dtifit -k data -m nodif_brain_mask -r bvecs -b bvals -m This one
> gave me an error, so I used GUI instead, which worked fine.
> The error messeage was, "terminate called after throwing an
> instance of 'Utilities::X_OptionError' what(): -m: unknown error!"
>
Yep sorry - a typo. Should have read
dtifit -k data -m nodif_brain_mask -r bvecs -b bvals -o dti
>
> I have additional questions, but this is specifically about fslview
> 1. When V1 image is displayed using RGB colormap in DTI mode, does
> it represent the maximum of the three coefficients? I can't seem
> to figure out how RGB colormap is assigned here.
Every colour on a screedn is a mixture of different quantities of
red, green and blue light. For the colurs you can see in RGB mode, we
just take the vector in question (usually V1), and set R=x, G=y, B=z
> 2. When V1 is modulated with FA, does it simply multiply V1 image
> with the FA(0~1)?
>
Yes that's right
T
> Thanks again,
>
> With regards,
>
> Hedok
>
>
>
>
>> 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 -0.180284493 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!
>>>
>>>
|