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Hi,
Thanks for the reply.
My input data (i.e. con_001_dti_data_FA.nii.gz etc) is in neurological format. I see from data formats and orientation page that “we do not recommend using anything but radiologically ordered images with this release”. Yet, a few posts ago Mark advised that “There should be no problem at all using neurologically-ordered or radiologically-ordered data in the latest version of FSL (4.1.4).”
I am wondering if the problems I’m having are in fact, because I’m using neurological images with tbss_2_reg?
When I use fslswapdim and then swaporient on my mean_FA image, this still does not alleviate the problem with overlaying the MNI 1mm brain – oddly the “swapdim+swaporient” image has the same labels as the original and looks exactly the same as it. And again, when the MNI 1mm brain is overlayed on this “swapdim+swaporient” image, it is not aligned to MNI space. The “swapdim+swaporient” image does however return “neurological” after fslorient -getorient, whereas the original mean_FA image is “radiological”.
In short, I’m wondering whether most of this mix-up is due to the neurological format of the con_001_dti_data_FA images that are fed into tbss-2_reg - - and if so, is the only way around this just to change them all with fslswapdim and swaporient and start over?
Thanks,
Laurence
HI - I'm guessing that means that the input data may not have had valid NIFTI headers?
If the FSL page about formats
http://www.fmrib.ox.ac.uk/fsl/fsl/formats.html
and the FAQ don't help, use fslswapdim etc. to get all your input data into the same orientation as the MNI standard space images, making sure not to get L-R swapped wrongly. Check in FSLView that the apparent orientation, and the labels, are all the same as the MNI images.
Once this is all done, hopefully you should have no further problems with the TBSS scripts?
Cheers.---------------------------------------------------------------------------
On 8 Sep 2009, at 11:41, Laurence O'Dwyer wrote:
Hi,
I have two queries about tbss:
(1)After running a number of preliminary tbss runs I’m continuing to have
problems with the orientation of the images after tbss_2_reg – all images
are incorrectly labelled with P in anterior areas and A in Posterior areas.
Overlaying the MNI shows that tbss_2_reg images are reversed in relation to
MNI. I’m still unsure why this is happening and how to correct it.
(2)Once the stats folder is created, how is it possible to calculate the
mean global FA values for each group, i.e. for control and patient group? I
presume this should be a straightforward procedure but I can’t find any
reference to it in the tbss manual.
Thanks,
Laurence
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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