Hi again,
Didn't rescan, as suggested, and used the diffusion mask (although had
to rename the output file to nodif as bedpostx requires this naming to
process). Now I get this error:
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect
- *PLEASE CHECK*!
Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
Any ideas? Could be differences in voxel dimensions? FoV?
Vasileios.
On 07/05/2016 12:48 μμ, Stamatios Sotiropoulos wrote:
> No need to rescan. You should simply get a mask from the diffusion data, not the T1.
>
> Cheers
> Stam
>
>
>> On 7 May 2016, at 10:38, Vasileios Kokkinos <[log in to unmask]> wrote:
>>
>> Hi Stam,
>>
>> Thanx for the swift response.
>>
>> Already done that through BET and the error persists. But it seems that it needs an exact match, right? The whole-brain T1 mask should fully correspond to the diffusion acquisition brain. Even a single slice off can produce a mismatch. This wasn't the case in Neuro3D, as it would coregister structural and tensor data without 100% overlap. Obviously scanning has to adapt to FSL as well.
>>
>> I'll rescan with whole-brain DTI and give it a go anew.
>>
>> Thanx.
>> Vasileios.
>>
>>
>> On 07/05/2016 12:21 μμ, Stamatios Sotiropoulos wrote:
>>> Hi Vasileios
>>>
>>> Yes you need a mask that matches your diffusion data. You can get that by running bet on the data. Have a look at the online documentation for more details.
>>>
>>> Cheers
>>> Stam
>>>
>>>
>>>
>>>
>>>> On 7 May 2016, at 09:50, Vasileios Kokkinos <[log in to unmask]> wrote:
>>>>
>>>> Hi everyone,
>>>>
>>>> I have been working for years with Siemens' Neuro3D for tractography at the clinic and only recently kicked off with FSL in order to process data from other scanners. So I stumbled upon this problem, and I'd appreciate any help, if anyone has come across it as well.
>>>>
>>>> I get a kill during the estimation process by BEDPOSTX (with default settings). At some point during the post-processing stage, the process halts, and pops up the error message: "Errors: child killed: kill signal" and prompts to the log file, where the error is:
>>>>
>>>> Image Exception : #3 :: Mask of different size used in matrix()
>>>> An exception has been thrown
>>>> Mask of different size used in matrix()
>>>>
>>>> Could it be the fact that the diffusion acquisition is not whole brain and crops a bit of cortex on the top, thereby making the structural mask (derived from a T1 whole-brain scan) incompatible?
>>>>
>>>> Could it be that the diffusion images are weighted (2)? Or could it be the effect of other acquisition parameters that FSL regards are pre-set?
>>>>
>>>> The acquisition settings for the DTI are below:
>>>> TR:8000, TE: 94, 50 slices, 2x2x2, A->P phase encoding, dist fact 0%, 6 averages 1 concatenation in a single series, iPat GRAPPA acc.f: 2, axial orientation, MDDW diffusion mode, Diff weighting 2, b1:0, b2:1000.
>>>>
>>>> Any idea or help would be most appreciated.
>>>>
>>>> Vasileios Kokkinos
