Yuko, Doug,

I think if you reoriented your images correctly in spm, then fsl should 
read them all right, there should be no need to reslice (which is always 
detrimental to data quality).

There are different places in the header where image orientation can be 
encoded, for example representing voxel space (the space in which the 
image was acquired in) and world space (some other space :). If you 
import your images, they are in voxel space. If you then reorient them, 
they will have a mapping to world space in their header. The main 
culprit here is that it is *not* sufficient to reorient the images using 
the display function, you also need to apply the reorientation to the image.

If you want to try, make a copy of some newly imported image and
- load it using display
- on the lower right, switch between "voxel space" and "world space" 
(likely no difference)
- rotate the image by entering, say, 1 for yaw
- close the graphics window (or call up another image or whatever)
- display the image again (you will see that nothing has changed)
- now enter -1 for yaw
- click on "reorient images" and select the image, click done
- the image will now be reoriented by encoding the new positional 
information in the header (one big thing I still like about using 
img/hdr files is that you can immediately see that only the header was 
adapted, while the image file remains untouched)
- now switch again between "voxel space" and "world space": big 
difference :)

Hope this helps,
Marko

Yuko wrote:
> Dear Doug,
>
> Thank you so much for your advice.
> Can I use reslice_nii.m function with SPM8?
> If so, should I execute "realign and reslice" for the original T1 image
> using reoriented T1 image as reference image?
>
> Thank you very much for your time.
>
> Best,
> Yuko
>
>
>
> 2014-04-08 16:36 GMT-04:00 Douglas Merkitch <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
>     Hello Yuko,
>
>     I believe that we have solved similar problems using the
>     reslice_nii.m function (its default output is in the RAS aka
>     neurological orientation).
>
>     Hope this helps,
>
>     Doug Merkitch
>     Neurological Sciences
>     Rush University Medical Center
>     Phone: (312) 563-3853 <tel:%28312%29%20563-3853>
>     Fax: (312) 563-4660 <tel:%28312%29%20563-4660>
>     Email: [log in to unmask] <mailto:[log in to unmask]>
>
>
>
>     On Apr 8, 2014, at 3:21 PM, Yuko <[log in to unmask]
>     <mailto:[log in to unmask]>>
>       wrote:
>
>>     Dear John,
>>
>>     Thank you so much for your prompt reply.
>>
>>     I did dicim import twice. But the image orientation was wrong.
>>     So, I fixed it with "Display" function.
>>
>>     I tried to look the anatomical images with fslview. But the image
>>     orientation of the images that I corrected were still wrong.
>>     So I wonder if I fixe the image orientation with "Display', I
>>     can't use it with FSL or other software.
>>
>>     It would be great if you would let me know something about this.
>>
>>     Best regard,
>>     Yuko
>>
>>
>>
>>     2014-04-08 14:33 GMT-04:00 John Ashburner <[log in to unmask]
>>     <mailto:[log in to unmask]>>:
>>
>>         If you use the DICOM button of SPM, this should convert the
>>         original DICOM into NIfTI so that you get the right
>>         orientation.  The conversion works for most scans, although
>>         data from some scanners is occasionally problematic.  DICOM is
>>         very flexible, and scanner manufacturers sometimes extend the
>>         format for their own purposes.  Because I have only had access
>>         to a relatively small number of datasets from different
>>         scanners for testing the conversion code, it is likely that
>>         there are some files that may not be handled so well.
>>
>>         First of all, make sure that the data are actually oriented
>>         incorrectly.  Depending on what software you use to visualise
>>         the data, the images may appear upside down.
>>
>>         Also, check that the data are actually flipped.  It's possible
>>         that they have just been rotated by 180 degrees.  This is very
>>         difficult to assess without some form of MR visible marker on
>>         the subject's head.
>>
>>         If you don't have access to the original DICOM files, then you
>>         can use the Display button, enter various rotations (and
>>         possibly some zooms of -1) until you have the NIfTI image
>>         shown in the correct orientation, then click the "Reorient
>>         images..." button to actually change the orientation of the
>>         NIfTI files on disk.
>>
>>         Best regards,
>>         -John
>>
>>
>>
>>
>>
>>         On 8 April 2014 19:20, Yuko <[log in to unmask]
>>         <mailto:[log in to unmask]>> wrote:
>>
>>             Dear SPM experts,
>>
>>             I've got anatomical images (T1).
>>             Those image orientation flipped, so anterior brain region
>>             located in posterior.
>>             I wonder if you could have any ideas to fix this wrong
>>             image orientation.
>>
>>             Any suggestion will be highly appreciated.
>>
>>             Thank you so much.
>>
>>             Yuko
>>
>>
>>
>
>

-- 
____________________________________________________
PD Dr. med. Marko Wilke
  Facharzt für Kinder- und Jugendmedizin
  Leiter, Experimentelle Pädiatrische Neurobildgebung
  Universitäts-Kinderklinik
  Abt. III (Neuropädiatrie)


Marko Wilke, MD, PhD
  Pediatrician
  Head, Experimental Pediatric Neuroimaging
  University Children's Hospital
  Dept. III (Pediatric Neurology)


Hoppe-Seyler-Str. 1
  D - 72076 Tübingen, Germany
  Tel. +49 7071 29-83416
  Fax  +49 7071 29-5473
  [log in to unmask]

  http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________