Hi - in both cases it looks like there's a problem with FLIRT, which I don't understand because if BET has worked well (looks like it has) and the image is in the right orientation to start with it is VERY rare for FLIRT not to work well and robustly.  Is it possible that maybe your voxel sizes are not set correctly in the header?

I'm afraid I'm now going to be away from email for the next 3 weeks travelling around China - so can't follow up on this - but maybe you should put your original structural images onto DropBox and someone might be able to look into the FLIRT question.

Cheers, Steve.

On 17 May 2012, at 03:43, Deanna Greene wrote:

Thank you for the quick reply.  

I tried to reorient the image, but it seems that it was already in the same orientation as the MNI152 template.  So when I ran sienax again (just to try), the standard space registration results are still oriented incorrectly.  Here is an image of the html output:  https://www.dropbox.com/s/fhp65rbcn60nf0w/sub1.pdf

For my second issue, here is an image of the html output:  https://www.dropbox.com/s/ca0n3ygprrek8ce/sub2.pdf

I am particularly worried about the anterior part of the brain that is being excluded from the whole brain segmentation, as can be seen in the sagittal and axial views.  How can I make sure the standard brain mask encompasses the entire brain?  

Thanks again!

-Deanna

On May 15, 2012, at 9:27 PM, Stephen Smith wrote:

Hi

On 16 May 2012, at 10:20, Deanna Greene wrote:

Dear FSL experts,

I am trying to normalize volumes by ICV in order to make group comparisons.  After looking through many threads on calculating ICV, it seems that using the VSCALING value from sienax as a normalization factor is the best approach.  So, I have run sienax on my subjects, but I am noticing problems with the output from some subjects.  

1.  For a few subjects, it appears that the individual structural scans are going into standard space in the wrong orientation.  The BET results look good (I think), but the FLIRT standard space registration results are oriented wrong.

The simplest thing to do is to reorient them by hand to have the right general orientation as the MNI152 template - you probably can run the same reorient command on all images.

If your header has enough orientation image, you can use fslreorient2std

2.  The other issue is that for about half of my subjects, the standard brain mask is smaller than the BET-derived brain mask (and smaller than the subject's brain).  Therefore, when I look at the "Field of view and standard space masking" in the html output, there is a ring of blue (from the BET-derived brain mask) showing the part of the BET mask that does not overlap with the standard space mask.  The result of this seems to be that the whole-brain segmentation cuts off part of the brain, so I imagine that the size of the brain is being underestimated, which worries me when using the VSCALING value.  

This sounds like the brain extraction of registration is not working well - without knowing more details, i couldn't say which.

You can put images on your website, dropbox, etc for people to see.

Cheers.

Does anyone know how I can fix these problems?  Also, if someone could tell me how to attach the images from the html output without exceeding the size limits for posts, that would be very helpful, as I think seeing the output would help convey the issues.

Thank you very much!
-Deanna

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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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