Hi everybody,
I've been running fslvbm on some datasets and I have an issue which
has me stumped, hopefully someone here can shed light on it for me.
I convert my original T1 images to RPI and place them in a directory,
then rescale them (using tbss_1_preproc). I then proceed to run
fslvbs_1_bet and fslvbm_2_template.
When I look in the results of the of fslvbm2a.[oe]* to see how the
segmentation went I see that fast is complaining about image flipping,
even though the original images were in RPI.
When I try to skull strip and segment the same data file by hand,
there is no complaint from fast about flipping. Likewise, when I copy
the ${subject}.anat_brain.{hdr,img} files into a separate directory
and run fast on it using the same arguments as in the fslvbm2a
script, I do not receive complaints from fast. This has me stumped.
Should I be concerned about the complaint about flipping during the
fslvbm_* pipeline Or can I safely ignore it?
If it would help I can make all the data available for download.
Regards,
--
Dr Colm G. Connolly
School of Psychology and Institute of Neuroscience
The Lloyd Building
University of Dublin
Trinity College, Dublin 2, Éire
Fax: +353-1-671-3183
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College Dublin, may be the
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