Dear FSLers and developers,
Congratulations on your new release. The installation went fine with my
machine so I decided to try out FIRST.
I have general questions about its usage and the images created by FIRST.
I ran “run_first_all im1 3 output_name” and my PC took about 2hrs to
finish. I haven’t tried “first_utils” yet, so my questions are regarding
the output image of first_all.
PC specification: AMD64 1.8GHz 2GM RAM Centos 64
#Q1 Would you recommend running bias-field correction before FIRST pipeline?
I didn’t find any recommendation on this in the website, so I appreciate if
you have any suggestion.
#Q2 Can I consider the output image as an alternative to ROI ?
After looking at the output image using FSL view, I thought I can create a
binary mask in each stricture, and apply them onto other modality like ADC
and FA as rough ROI. Is there something wrong with the concept here?
#Q3 When total volume is computed in each structure, does it consider
partial volume effect?
#Q4 The image intensity in the output image does not seem to correspond sub-
cortical label in the FSL website
(http://www.fmrib.ox.ac.uk/fsl/first/cma_subcortical_label.html). It
doesn’t seem to match with free-surfers’ colormap in “aseg” file either.
Correct me if I’m wrong. I appreciate if there is any look up table for
output intensity in the output image and anatomical labeling.
With regards,
Hedok
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