Hi
If you use the --showall option, then fslmeants will give you the
coordinates as well as the values of all voxels of your significant
cluster.
Saad.
On 19 Nov 2008, at 13:53, Stone, James (jrs7r) wrote:
> Hello,
> Thanks very much for this response. What is the best way to obtain
> the <yourClusterInSkeleton> values referred to below? Would this
> involve noting individual coordinates in FSLview or is there some
> automated method of creating a table of statistically significant
> clusters for a given skeleton?
> Thanks,
> James
>
>
> On 11/19/08 4:26 AM, "Saad Jbabdi" <[log in to unmask]> wrote:
>
> Hi James
> You can get mean FA values _on the skeleton_ for each subject using
> fslmeants:
> e.g.: fslmeants -i all_FA_skeletonised -m <yourClusterInSkeleton> -o
> <outputTextFile>
>
> You need to do that on the _non-filled_ cluster. No need for using
> tbss_deproject if this is all you want.
> You may also use the option --showall if you want to see FA values in
> all the voxels of your cluster.
>
> Cheers,
> Saad.
>
>
> On 18 Nov 2008, at 18:11, James Stone wrote:
>
>> I am in the processing of transitioning from data analyses with SPM
>> to
>> analyses with FSL and was hoping for some guidance on tools to use
>> for a
>> task at hand. I am in the process of evaluating a set of military
>> service
>> members exposed to repetitive low-level explosive blast to determine
>> if
>> their fractional anisotropy values change either before or after
>> training,
>> or are different between several groups entering this study with a
>> previous
>> history of differing levels of exposure. Here are the steps I have
>> taken so far:
>>
>> 1. Acquire diffusion data (in 30 directions and 2.5 mm slices)
>> 2. Convert dicom to nifti files
>> 3. Peform eddy correction
>> 4. Fit diffusion tensors using DTIFIT
>> 5. Run the tbss_1_preproc, tbss_2_reg -T, tbss_3_postreg,
>> tbss_4_prestats,
>> and suggested randomise steps in the TBSS documentation
>> instructions. I then
>> ran the tbss_fill step to fill out the local tracts for display
>> purposes.
>>
>> So I now have a dataset which nicely demonstrates where areas of
>> statistical
>> significance exist when comparing study groups. What I really need
>> at this
>> point to complete the dataset is to be able to go into the specific
>> clusters
>> which are significantly different determine corresponding mean FA
>> values
>> within clusters for each subject in the study.
>>
>> I see the documentation on "Transforming TBSS results back to native
>> space",
>> and can certainly follow these instructions, but I am not entirely
>> sure how
>> to get to mean FA values within a given cluster of statistically
>> significantly different voxels. What I am shooting for is data
>> similar to
>> the Giorgio et al. Neuroimage article (NeuroImage 39 (2008) 52-61).
>> Thanks in
>> advance for any help you might be able to provide with this.
>>
>
> Saad Jbabdi
> Oxford University FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222545 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
|