Hi,
I am also experiencing the same problem, and the only version of fsl on my
computer is 4.1.2.
I have worked around the problem by setting my threshold for the at 2000
(however, I am not 100% confident that this is appropriate because the
FA_all volumes do have values that range from 0-1).
I'm having difficulty with the previous step as well. When I visualize the
FA_all and FA_mean_skeleton together the skeleton extends beyond the range
of the FA_all stacks. It appears to be delineating white matter that would
be there if the stacks hadn't been masked. Should this be happening? And
will it effect my results? I've attached a photo to better demonstrate
what's happening.
Thanks experts!
Dylan
On Fri, 6 Mar 2009 23:25:56 +0100, Kathrine Skak Madsen <[log in to unmask]>
wrote:
>Well, I guess you could check your path with the "which" command, whether
>it points you to the tbss scripts in fsl-4.1.2/bin/
>
>e.g. which tbss_1_preproc
>
>Kathrine
>
>
>
>> Hi Kathrine, I just checked I use fsl 4.1.2 and ran the analysis
>> yesterday. How can I check the TBSS version?
>>
>> Michael
>>
>>
>> On 6-Mar-09, at 11:33 AM, Kathrine Skak Madsen wrote:
>>
>>> Hi Michael,
>>>
>>> It seems like your data have been analysed with the old TBSS version.
>>>
>>> In the old TBSS version (TBSS 1.1, FSL 4.0), the FA data were scaled
>>> to be
>>> between 0-10000 in tbss_1_preproc, whereas there is no scaling (FA is
>>> between 0-1) in the new TBSS version (1.2, FSL 4.1).
>>>
>>> Best wishes
>>> Kathrine
>>>
>>>
>>>> Hi fsl experts, I was just following the tbss instructions and wanted
>>>> to check after <tbss_3_postreg -T> if the threshold of 0.2 is good.
>>>> <fslview all_FA -b 0,0.8 mean_FA_skeleton -b 0.2,0.8 -l Green>
>>>>
>>>> I played around with the threshold in mean_FA_skeleton and nothing
>>>> really changend and then I realized that the values range in the
>>>> thousands.
>>>>
>>>> fslstats mean_FA_skeleton.nii.gz -R
>>>> 0.000000 8676.000000
>>>> fslstats mean_FA_skeleton.nii.gz -r
>>>> 2038.859985 7617.527832
>>>>
>>>> Any ideas?
>>>>
>>>> Michael
>>>>
>>
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