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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