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