Hi - for some reason, I haven't been getting FSL emails. Sorry.
This is a common problem. It happens because there is no carriage
return at the end of your bvals/bvecs files, or because your bvecs/
bvals files were made in Windows (on e.g. notepad of word) and have
lots of spurious Windows style carriage returns in them.
If you fix these file to be nothing but raw text, and put unix style
carriage returns at the end of every line (including the last one),
it will be fixed.
Cheers
T
On 21 Jan 2007, at 03:19, Stephen Smith wrote:
> Hi - if you want to send us the bvecs, bvals and input data files
> we can have a quick look.
>
> 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.
>
> Cheers.
>
>
>
> On Sat, 20 Jan 2007 12:43:15 -0000, Suzanna Laycock
> <[log in to unmask]> wrote:
>
>> Hi,
>>
>> Changing the display range doesn't seem to do anything, and trying
>> to get a
>> histogram crashes fslview ;-(
>>
>> Any other suggestions?
>> Suzanna
>> ------
>>
>> Does the FA image look ok if you change the FSLView display
>> range to 0:1? What does the histogram look like? Cheers
>>
>> On Fri, 19 Jan 2007 16:06:45 -0000, Suzanna Laycock
>> <[log in to unmask]> wrote:
>>
>>> Thanks - that's worked, and has generated all the relevant files.
>>>
>>> However, if I open dti_FA (and some others) in MRIcro or FSL_View,
>>> there doesn't appear to be an image, although the .img file has
>>> 4480KB
>>> of data in it. The dti_S0 file opens in MRIcro and produces an
>>> image.
>>>
>>> Any suggestions?
>>>
>>> Thanks in advance
>>> Suzanna
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library
>>> [mailto:[log in to unmask]] On Behalf Of Andreas Bartsch
>>> Sent: 19 January 2007 15:19
>>> To: [log in to unmask]
>>> Subject: [FSL] AW: [FSL] Running DTIFIT
>>>
>>>
>>> Hi,
>>>
>>> The bvals / bvecs seem to be recognized as directories. Your
>>> files are *.txt's so try mv bvals.txt bvals mv bvecs.txt bvecs
>>> And run again.
>>> Cheers-
>>> Andreas
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>> Im Auftrag von Suzanna Laycock
>>> Gesendet: Freitag, 19. Januar 2007 16:14
>>> An: [log in to unmask]
>>> Betreff: [FSL] Running DTIFIT
>>>
>>> Hi,
>>>
>>> I'm having problems running dtifit, and get the following error
>>> message. My files are saved in analyze format. In my subject
>>> folder, I have individual files for data, bvecs.txt, bvals.txt,
>>> nodif, nodif_brain_mask.
>>>
>>> $ dtifit -k data -r bvecs -b bvals -m nodif_brain_mask -o dti 0
>>> 128 0 128 0 70 0 slices processed Aborted (core dumped)
>>>
>>> Running bedpost_datacheck (as seems to be advised in the
>>> previous archives) produces this.
>>>
>>> Suzanna@suzanna /usr/local/fsl/bin
>>> $ bedpost_datacheck ~/FSL_DATA/99027 /home/Suzanna/FSL_DATA/99027/
>>> data
>>> dim1 128
>>> dim2 128
>>> dim3 70
>>> dim4 35
>>> datatype 4
>>> pixdim1 -1.7500000000
>>> pixdim2 1.7500000000
>>> pixdim3 2.0000000000
>>> pixdim4 1.0000000000
>>> cal_max 0.0000
>>> cal_min 0.0000
>>> glmax 0
>>> glmin 0
>>> origin1 0
>>> origin2 0
>>> origin3 0
>>> file_type ANALYZE-7.5
>>>
>>> /home/Suzanna/FSL_DATA/99027/nodif
>>> dim1 128
>>> dim2 128
>>> dim3 70
>>> dim4 1
>>> datatype 4
>>> pixdim1 -1.7500000000
>>> pixdim2 1.7500000000
>>> pixdim3 2.0000000000
>>> pixdim4 1.0000000000
>>> cal_max 0.0000
>>> cal_min 0.0000
>>> glmax 0
>>> glmin 0
>>> origin1 0
>>> origin2 0
>>> origin3 0
>>> file_type ANALYZE-7.5
>>>
>>> /home/Suzanna/FSL_DATA/99027/nodif_brain_mask
>>> dim1 128
>>> dim2 128
>>> dim3 70
>>> dim4 1
>>> datatype 4
>>> pixdim1 -1.7500000000
>>> pixdim2 1.7500000000
>>> pixdim3 2.0000000000
>>> pixdim4 1.0000000000
>>> cal_max 1.0000
>>> cal_min 0.0000
>>> glmax 0
>>> glmin 0
>>> origin1 0
>>> origin2 0
>>> origin3 0
>>> file_type ANALYZE-7.5
>>>
>>> num lines in /home/Suzanna/FSL_DATA/99027/bvals
>>> cat: /home/Suzanna/FSL_DATA/99027/bvals: Is a directory 0 num
>>> words in /home/Suzanna/FSL_DATA/99027/bvals
>>> cat: /home/Suzanna/FSL_DATA/99027/bvals: Is a directory 0 num
>>> lines in /home/Suzanna/FSL_DATA/99027/bvecs
>>> cat: /home/Suzanna/FSL_DATA/99027/bvecs: Is a directory 0 num
>>> words in /home/Suzanna/FSL_DATA/99027/bvecs
>>> cat: /home/Suzanna/FSL_DATA/99027/bvecs: Is a directory 0
>>> cat: /home/Suzanna/FSL_DATA/99027/bvals: Is a directory
>>> cat: /home/Suzanna/FSL_DATA/99027/bvecs: Is a directory
>>> cat: /home/Suzanna/FSL_DATA/99027/bvecs: Is a directory Runtime
>>> error (func=(main), adr=3): Divide by zero
>>> /usr/local/fsl/bin/bedpost_datacheck: line 48: [: -ne: unary
>>> operator expected number of elements in bvals is not equal to
>>> number of vols in data
>>> /usr/local/fsl/bin/bedpost_datacheck: line 54: [: -ne: unary
>>> operator expected
>>>
>>> Any suggestions? Sorry, my computer skills are pretty poor!
>>>
>>> Thanks
>>> Suzanna
> ===========================================================
>> =============
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