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
|
