Hi,

Yes, there are *very* different!
Are the labels in FSLView correct for each of them?

If so, then this error is a fundamental problem and you
need to fix the images before moving on.  I would
rarely recommend using fslcreatehd to make a new
image, as it is normally best to take an existing image
and use that (zeroing the intensities and filling them
with other things) just in order to get the orientation
information consistent.

If the FSLView labels are not correct then the orientation
information needs to be fixed in the images.

Have a look at this and also at your scripts.
This error has certainly saved you from a problem
in the pipeline in this case!

All the best,
	Mark


On 9 Jul 2010, at 14:55, wolf zinke wrote:

> Hi Mark,
>
> attached are two files with the output of fslhd. Indeed they show a  
> difference, which is getting even more puzzling for me. In the  
> preprocessing I create a new header with fslcreatehd, and both  
> images should be alligned to this header via a flirt command with  
> the reference image being the one with the new header. But maybe I  
> oversee something there at the moment, since I use several custom  
> scripts that I need to go through more carefully to identify a  
> possible reason of this difference. If necessary, I can check this  
> to figure out, why the headers become different.
>
> Thanks,
> wolf
>
> Mark Jenkinson wrote:
>> 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
>>>>>>
>>>>
>>>
>
> filename       scan_08_pp_dilmask.nii.gz
>
> sizeof_hdr     348
> data_type      UINT8
> dim0           3
> dim1           50
> dim2           60
> dim3           40
> dim4           1
> dim5           1
> dim6           1
> dim7           1
> vox_units      mm
> time_units     s
> datatype       2
> nbyper         1
> bitpix         8
> pixdim0        0.0000000000
> pixdim1        1.5000000000
> pixdim2        1.5000000000
> pixdim3        1.5000000000
> pixdim4        1.0000000000
> pixdim5        0.0000000000
> pixdim6        0.0000000000
> pixdim7        0.0000000000
> vox_offset     352
> cal_max        1.0000
> cal_min        0.0000
> scl_slope      0.000000
> scl_inter      0.000000
> phase_dim      0
> freq_dim       0
> slice_dim      0
> slice_name     Unknown
> slice_code     0
> slice_start    0
> slice_end      0
> slice_duration 0.000000
> time_offset    0.000000
> intent         Unknown
> intent_code    0
> intent_name
> intent_p1      0.000000
> intent_p2      0.000000
> intent_p3      0.000000
> qform_name     Aligned Anat
> qform_code     2
> qto_xyz:1      -1.499111  0.023354  0.046047  34.313286
> qto_xyz:2      0.021825  1.499017  -0.049729  -31.446194
> qto_xyz:3      0.046791  0.049029  1.498468  -7.431565
> qto_xyz:4      0.000000  0.000000  0.000000  1.000000
> qform_xorient  Right-to-Left
> qform_yorient  Posterior-to-Anterior
> qform_zorient  Inferior-to-Superior
> sform_name     Aligned Anat
> sform_code     2
> sto_xyz:1      -1.498825  0.014839  0.048229  34.313286
> sto_xyz:2      0.029876  1.552485  -0.083700  -31.446194
> sto_xyz:3      0.044101  0.015507  1.490551  -7.431565
> sto_xyz:4      0.000000  0.000000  0.000000  1.000000
> sform_xorient  Right-to-Left
> sform_yorient  Posterior-to-Anterior
> sform_zorient  Inferior-to-Superior
> file_type      NIFTI-1+
> file_code      1
> descrip        FSL4.0
> aux_file
> filename       scan_08_pp_norm.nii.gz
>
> sizeof_hdr     348
> data_type      FLOAT32
> dim0           4
> dim1           50
> dim2           60
> dim3           40
> dim4           750
> dim5           1
> dim6           1
> dim7           1
> vox_units      mm
> time_units     s
> datatype       16
> nbyper         4
> bitpix         32
> pixdim0        0.0000000000
> pixdim1        1.5000000000
> pixdim2        1.5000000000
> pixdim3        1.5000000000
> pixdim4        1.8300000429
> pixdim5        0.0000000000
> pixdim6        0.0000000000
> pixdim7        0.0000000000
> vox_offset     352
> cal_max        1891.9297
> cal_min        0.0000
> scl_slope      1.000000
> scl_inter      0.000000
> phase_dim      0
> freq_dim       0
> slice_dim      0
> slice_name     Unknown
> slice_code     0
> slice_start    0
> slice_end      0
> slice_duration 0.000000
> time_offset    0.000000
> intent         Unknown
> intent_code    0
> intent_name
> intent_p1      0.000000
> intent_p2      0.000000
> intent_p3      0.000000
> qform_name     Scanner Anat
> qform_code     1
> qto_xyz:1      -1.496775  -0.070926  -0.068066  47.211300
> qto_xyz:2      0.071224  -0.066591  -1.496828  11.907200
> qto_xyz:3      -0.067754  1.496842  -0.069816  -25.746901
> qto_xyz:4      0.000000  0.000000  0.000000  1.000000
> qform_xorient  Right-to-Left
> qform_yorient  Inferior-to-Superior
> qform_zorient  Anterior-to-Posterior
> sform_name     Scanner Anat
> sform_code     1
> sto_xyz:1      -1.531990  -0.090340  -0.069169  47.211300
> sto_xyz:2      0.071405  -0.062002  -1.513580  11.907200
> sto_xyz:3      -0.047566  1.467970  -0.073048  -25.746901
> sto_xyz:4      0.000000  0.000000  0.000000  1.000000
> sform_xorient  Right-to-Left
> sform_yorient  Inferior-to-Superior
> sform_zorient  Anterior-to-Posterior
> file_type      NIFTI-1+
> file_code      1
> descrip        FSL4.0
> aux_file