Dear Mark,
i ran both "avwswapdim input -x y z output" and "avworient -swaporient
output" on one fMRI volume. but, when i look at the flipped one, and the
original one in fslview, there is no difference (picture at
http://web.mit.edu/paymon/www/neurological_vs_radiological_fsl.bmp).
this does not seem normal. any idea on how i should fix this?
thanks a lot,
paymon
Paymon Hosseini wrote:
> Dear Mark,
> The fMRI results are consistent across level1, level2, and level3:
> activations are always on the right side when they should be on the
> left side. Hence, i doubt there is a problem in the processing stream.
>
> Just to double check, what i need to do is run
> 1) avwswapdim input -x y z output
> 2) avworient -swaporient output
> on all initial volumes (structural and functional) and re-run the
> analysis?
>
> thanks a lot,
> paymon
>
> ps.
>
> To be complete, here is the output of avwhd for the same volume on
> which i ran mri_info.
> >> avwhd enc_1_fmri.nii.gz
> filename enc_1_fmri.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 64
> dim2 64
> dim3 25
> dim4 208
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 3.1250000000
> pixdim2 3.1250000000
> pixdim3 5.0000000000
> pixdim4 2.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 352
> cal_max 0.0000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -3.124882 0.002344 -0.043309 98.407486
> qto_xyz:2 0.002344 -3.078467 -0.859630 150.438263
> qto_xyz:3 -0.027068 -0.537269 4.925359 -16.791046
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -3.124881 0.000000 -0.043635 98.407486
> sto_xyz:2 0.004689 -3.078467 -0.859615 150.438263
> sto_xyz:3 -0.026864 -0.537278 4.925360 -16.791046
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Anterior-to-Posterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FreeSurfer Aug 13 2006
> aux_file
>
>
>
>
>
> Mark Jenkinson wrote:
>> Dear Paymon,
>>
>> Is it the case that the first level results are correctly labeled?
>> There really should not be a change between the first and second
>> level results (or third level for that matter). If this is happening
>> then something seriously wrong is occurring.
>>
>> I'm also not sure why "it seems like the data are in radiological
>> convention".
>> FSLView always displays images in this convention (as much as the
>> original orientation will allow) but what we mean by "radiological"
>> and "neurological" is about data ordering (see FSL FAQ) and the
>> result returned by avworient is the true answer to this.
>>
>> Unfortunately, I am not familiar with the output from mri_info
>> so I cannot comment on these. Output from avwhd is more
>> useful to us.
>>
>> The bottom line though is that if your images are not oriented
>> correctly, then you need to fix this. If it occurs in all levels of
>> Feat then you probably just need to fix the original images
>> (and re-run the analyses). If it is OK at first level but then
>> goes wrong then something is not working correctly and we
>> will need to find the problem. If this is the case, please tar
>> up your feat directory (and input files) and send them to
>> us via our upload site at:
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>> and send us the reference number of the upload.
>>
>> All the best,
>> Mark
>>
>>
>>
>>
>>
>>
>> On 16 Oct 2006, at 02:42, Paymon Hosseini wrote:
>>
>>> Dear Mark,
>>>
>>> I have decided that my fMRI volumes are left/right flipped because
>>> my stimuli are verbal, yet all the 3rd level activations in FSL are
>>> on the right side of feat report images (tagged with "R", hence on
>>> the right side of the brain). It seems like the data are in
>>> radiological convention, but they are incorrectly tagged as being in
>>> neurological convention. Consistent with this idea, running
>>> "avworient -getorient" results in a "NEUROLOGICAL" output.
>>>
>>> what i still don't understand is if "it is absolutely necessary" to
>>> go back to the original volumes, flip them, and redo the entire
>>> analysis.
>>>
>>> thank you very much for your help,
>>> paymon
>>>
>>> ps.
>>>
>>> here is the information about about one fMRI slice before i fed it
>>> (and its comrades) to mri_convert to be converted to nii format:
>>> -------------
>>> >> mri_info f_019.bshort
>>> Volume information for f_019.bshort
>>> type: bshort
>>> dimensions: 64 x 64 x 25 x 208
>>> voxel sizes: 3.1250, 3.1250, 5.0000
>>> type: SHORT (4)
>>> fov: 200.000
>>> xstart: -100.0, xend: 100.0
>>> ystart: -100.0, yend: 100.0
>>> zstart: -62.5, zend: 62.5
>>> TR: 2000.00 msec, TE: 30.00 msec, TI: 30.00 msec, flip
>>> angle: 90.00 degrees
>>> nframes: 208
>>> ras xform present
>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0087, c_r
>>> = -2.1341
>>> : x_a = 0.0015, y_a = -0.9851, z_a = -0.1719, c_a
>>> = 41.3322
>>> : x_s = -0.0086, y_s = -0.1719, z_s = 0.9851, c_s
>>> = 26.7234
>>> Orientation : LPS
>>> Primary Slice Direction: axial
>>>
>>> voxel to ras transform:
>>> -3.1249 0.0000 -0.0436 98.4075
>>> 0.0047 -3.0785 -0.8596 150.4383
>>> -0.0269 -0.5373 4.9254 -16.7910
>>> 0.0000 0.0000 0.0000 1.0000
>>>
>>> voxel-to-ras determinant 48.8281
>>>
>>> ras to voxel transform:
>>> -0.3200 0.0005 -0.0028 31.3708
>>> 0.0000 -0.3152 -0.0550 46.4996
>>> -0.0017 -0.0344 0.1970 8.6526
>>> 0.0000 0.0000 0.0000 1.0000
>>> -------------------
>>>
>>>
>>>
>>> here is the information about the nii volume that includes the above
>>> slice
>>>
>>> -------------------
>>> >>avworient -getorient enc_1_fmri.nii.gz
>>> NEUROLOGICAL
>>>
>>> >> mri_info enc_1_fmri.nii.gz
>>> INFO: using NIfTI-1 sform
>>> Volume information for enc_1_fmri.nii.gz
>>> type: nii
>>> dimensions: 64 x 64 x 25 x 208
>>> voxel sizes: 3.1250, 3.1250, 5.0000
>>> type: SHORT (4)
>>> fov: 64.000
>>> xstart: -32.0, xend: 32.0
>>> ystart: -32.0, yend: 32.0
>>> zstart: -12.5, zend: 12.0
>>> TR: 2000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>> angle: 0.00 degrees
>>> nframes: 208
>>> ras xform present
>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0087, c_r
>>> = -2.1341
>>> : x_a = 0.0015, y_a = -0.9851, z_a = -0.1719, c_a
>>> = 41.3322
>>> : x_s = -0.0054, y_s = -0.1719, z_s = 0.9851, c_s
>>> = 26.7234
>>> Orientation : LPS
>>> Primary Slice Direction: axial
>>>
>>> voxel to ras transform:
>>> -3.1249 0.0000 -0.0436 98.4075
>>> 0.0047 -3.0785 -0.8596 150.4383
>>> -0.0168 -0.5373 4.9254 -17.1134
>>> 0.0000 0.0000 0.0000 1.0000
>>>
>>> voxel-to-ras determinant 48.8268
>>>
>>> ras to voxel transform:
>>> -0.3200 0.0005 -0.0028 31.3708
>>> -0.0002 -0.3152 -0.0550 46.4992
>>> -0.0011 -0.0344 0.1970 8.6538
>>> 0.0000 0.0000 0.0000 1.0000
>>>
>>> ------------------
>>>
>>>
>>>
>>> Mark Jenkinson wrote:
>>>> Dear Paymon,
>>>>
>>>> How are you deciding that the images have been flipped?
>>>> This is non-trivial to determine by looking at the images, and
>>>> there has been quite a lot of confusion in the past about
>>>> how to interpret image orientation. We now provide
>>>> labels in FSLView when the appropriate qform/sform settings
>>>> are contained in the nifti file. These labels are the best way
>>>> to tell how FSL is interpretting your images. We are very
>>>> careful internally to make sure that left-right is not flipped
>>>> during the processing, but we do register to the standard
>>>> space (or highres) images which can involve a large rotation
>>>> which can appear like a flip at first glance.
>>>>
>>>> Also, there are some problems with having images in
>>>> "neurological order" (see the FSL FAQ for the definition)
>>>> and if this is the case for your input images then I would
>>>> suggest changing them to "radiological order" as described
>>>> in the FSL FAQ.
>>>>
>>>> If you still think that there is an incorrect flip then please
>>>> provide us some details about the images and how you
>>>> have decided that a flip exists.
>>>>
>>>> All the best,
>>>> Mark
>>>>
>>>>
>>>>
>>>> On 14 Oct 2006, at 23:28, Paymon Hosseini wrote:
>>>>
>>>>> Dear FSL users,
>>>>>
>>>>> i apologize beforehand, because you have probably seen a variation
>>>>> of this question a million times.
>>>>>
>>>>> after getting to the second level of Feat multisession/multilevel
>>>>> analysis, i realized that the left/right orientations must have
>>>>> been flipped in my original volumes (converted from COR to nii
>>>>> using mri_convert). Because i am certain the volumes are flipped,
>>>>> I am wondering if it is necessary to reorient the data an repeat
>>>>> the analysis from scratch? Specifically, does this flipped
>>>>> orientation influence the registration of the original volumes to
>>>>> the standard avg brain, or is the orientation just a label?
>>>>>
>>>>> thanks a lot,
>>>>> Paymon
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