Dear JD -
Congratulations on choosing FSL - the only reasonable choice of diffusion analysis software. However, unfortunately you have found the wrong email list to send your queries to. Could you perhaps re-address this to the FSL list ([log in to unmask]).
Best
Tim
On 19 Jun 2012, at 07:39, SUBSCRIBE DIFFUSION Anonymous wrote:
> Dear FSL users,
>
> I’m new to FSL and DTI analysis and currently trying to work my way through the preprocessing and first steps of tractography of DTI data. I’m using fsl-4.1.9 and encountered problems/errors during the following steps. I have not found matching solutions on the internet or within the mailing archive (excuse me if I oversaw them), so I would be thankful for any help.
>
> Conversion from dicom to nifti:
> Warning: “diffusion acquisition does not have b-0 image, potential partial acquisition or improper segmentation of files, possible solution: use -c Y and use folder containing subdirectories as input or change .ini file to read: CollapseFolders=1”.
> The dti-sequence we use has 10 reference scans, so the b-0 doesn’t seem to be recognized by the program. All acquired DTI and mdeft images were in one folder. I used -c Y and set the default options of fsl, without improvement. Is there anything wrong with the information within the dicoms? And if so, can this be fixed?
>
> Eddy current correction:
> How can the mean of the 10 reference scans (b-0) be calculated to form a template for ECC? (Instead of just defining the first of the 10 b-0-volumes)
>
> Brain extraction:
> When I open my nodif_brain_mask in fslview, the mask is in “scanner-anatomical”-format and not in diffusion space. Is the diffusion space format a prerequisite for tractography? If so, how can the transformation be accomplished?
>
> Bedpostx:
> The datacheck seems to be fine.
> However, running bedpostx results in the warning that for some reason it does not have successfully completed. However, all files (merged_th<i>samples, merged_ph<i>samples, merged_f<i>samples, mean_th<i>samples, mean_ph<i>samples, mean_f<i>samples, mean_dsamples, mean_S0samples, dyads<i>, dyads<i>_dispersion, nodif_brain, nodif_brain_mask) are there. I ran it with n=2 fibres, weight w=1 and b=1000. How can be checked what went wrong?
>
> Tractography:
> Runs into segmentation fault.
>
> I would be really thankful for any reply, suggestion and help.
> Thank you for your effort and your time.
> Best regards,
> JD
>
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