Hi,
Can you send us the output of fslhd run on the following files:
/XTRA/tossi/morph_DMS/2009_03_05/scan_08/scan_08_pp_norm
and
/XTRA/tossi/morph_DMS/2009_03_05/scan_08/scan_08_pp_dilmask.nii.gz
It is possible that these have either slightly different coordinate
definitions,
in which case there is nothing to worry about, or they are seriously
different in which case there is a problem.
This is a new warning in 4.1.6 that is explicitly designed to detect
such
problems, but is possibly too sensitive.
If you send us the fslhd output above then I will be able to decide.
All the best,
Mark
On 8 Jul 2010, at 19:05, wolf zinke wrote:
> Hi,
>
> I noticed that the same warning occurs also for the post stats,
> indicating that there is something with my mask. Anyway, since this
> is just a dilated mask I don't think that this is a serious problem.
> But still strange why this now appears. Is there a new test routine
> in the new FSL patch that explains that I never noticed this warning
> before?
>
> thanks,
> wolf
>
> /GLOCAL/fsl/bin/fslmaths thresh_zstat1 -mas /XTRA/tossi/morph_DMS/
> 2009_03_05/scan_08/scan_08_pp_dilmask.nii.gz thresh_zstat1
>
> WARNING:: Inconsistent orientations for individual images in pipeline!
> Will use voxel-based orientation which is probably incorrect
> - *PLEASE CHECK*!
>
>
> wolf zinke wrote:
>> Hi Mark,
>>
>> Sure I can give you the log file. I attached the whole file.
>>
>> Thanks for the help,
>> wolf
>>
>>
>>
>> Mark Jenkinson wrote:
>>> Hi,
>>>
>>> This might be serious but probably isn't.
>>> Can you send the appropriate portion of the log file so
>>> that we can see the context of when this warning occurs?
>>>
>>> All the best,
>>> Mark
>>>
>>> On 8 Jul 2010, at 18:03, wolf zinke wrote:
>>>
>>>> Hi
>>>>
>>>> I run a batch of feat analyses on the same subject. So in
>>>> principle everything should be the same for each analysis (except
>>>> the functional volume and the event files of course). However, I
>>>> get now warnings in the feat2_pre logfile:
>>>>
>>>> WARNING:: Inconsistent orientations for individual images in
>>>> pipeline!
>>>> Will use voxel-based orientation which is probably
>>>> incorrect - *PLEASE CHECK*!
>>>>
>>>> Is this a new feature of the patch? What exactly does this mean,
>>>> and what am I supposed to check now? I would be highly confused
>>>> if this means, that there is something like a left-right flip in
>>>> the data (it should be everythere in such a case).
>>>>
>>>> Any pointer to help me out?
>>>>
>>>> Thanks a lot,
>>>> wolf
>>>>
>>
>
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