Thank you! We think this was the problem. When we look at other subjects we ran bedpost on, we see 72 slices for the files. This 1st subject is missing some slices for files in the output.bedpostx directory. We'll run probtrackx on other subjects, and update our progress.
Thanks again,
D. Michael
On Mon, 29 Apr 2013 14:30:22 +0100, Saad Jbabdi <[log in to unmask]> wrote:
>Hi - Yes it looks like bedpostx failed to produce a few slices in your image (assuming your original data had 72 slices).
>
>You need to re-run bedpostx I am afraid.
>
>
>Cheers
>Saad.
>
>
>On 29 Apr 2013, at 14:22, D. Michael <[log in to unmask]> wrote:
>
>> Hello,
>>
>> Thank you for your response and suggestion.
>>
>> Just doing a quick check:
>>
>> fslsize nodif_brain_mask.nii.gz
>> dim1 128
>> dim2 128
>> dim3 72
>> dim4 1
>> pixdim1 1.7968750000
>> pixdim2 1.7968750000
>> pixdim3 2.0000000000
>> pixdim4 1.0000000000
>>
>>
>> fslsize merged_ph2samples.nii
>> dim1 128
>> dim2 128
>> dim3 63
>> dim4 50
>> pixdim1 1.7968750000
>> pixdim2 1.7968750000
>> pixdim3 2.0000000000
>> pixdim4 1.0000000000
>>
>>
>> fslsize mean_f1samples.nii.gz
>> dim1 128
>> dim2 128
>> dim3 63
>> dim4 1
>> pixdim1 1.7968750000
>> pixdim2 1.7968750000
>> pixdim3 2.0000000000
>> pixdim4 1.0000000000
>>
>>
>>
>> If you look at dim3 for the first 2 files, they differ. And for the latter 2 files, hey differ in dim4 size.
>>
>> Could this be the issue, and what would be the cause? Is bedpostx producing something incorrectly? Or is it something with the nodif_brain_mask?
>>
>>
>> D. Michael
>>
>> On Mon, 29 Apr 2013 14:06:31 +0100, Saad Jbabdi <[log in to unmask]> wrote:
>>
>>> Hi
>>> Can you check that all nifti files in your bedpostx directory have the same image size (with fslsize).
>>>
>>> Cheers
>>> Saad
>>>
>>>
>>> On 29 Apr 2013, at 13:44, D. Michael <[log in to unmask]> wrote:
>>>
>>>> Hello,
>>>>
>>>> We are having issues running probtrackx. We are using FSL 5.02 through the debian package on Ubuntu 10.04.
>>>>
>>>> Every time attempt to run it, we get this output:
>>>>
>>>> rm -rf /probtrackdirectory
>>>> mkdir -p /probtrackdirectory
>>>> /probtrackdirectory/fdt_script.sh
>>>>
>>>>
>>>> However, nothing seems to run. We checked the fdt_script.sh.e67 file and it reads this:
>>>>
>>>> Image Exception : #3 :: Mask of different size used in matrix()
>>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>>>> Aborted (core dumped)
>>>>
>>>> Not sure what exactly is going here. Anyone experience similar problems? Any help would be appreciated.
>>>>
>>>> Thanks,
>>>>
>>>> D. Michael
>>>>
>>>
>>> --
>>> Saad Jbabdi
>>> University of Oxford, FMRIB Centre
>>>
>>> JR Hospital, Headington, OX3 9DU, UK
>>> (+44)1865-222466 (fax 717)
>>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>--
>Saad Jbabdi
>University of Oxford, FMRIB Centre
>
>JR Hospital, Headington, OX3 9DU, UK
>(+44)1865-222466 (fax 717)
>www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
>
>
>
>
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