Hi Élodie
if you upload your subject we will take a look
cheers
Bruce
On Fri, 1 Jul 2016, Elodie
Cauvet wrote:
Dear Freesurfer list,
Sorry to bother by posting again, but I am bit stuck by this issue and would
be really glad to get some help on that issue. Of course I can upload some
data if needed.
Thanks a lot!
Maybe I am hoping for a miracle with my question, but I am bit desperate
after unsuccessfully trying things around for over a year.
In a nutshell, I need advice on the intensity normalization options.
We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner
with a 32 channel coil (IR-FSPGR 3D volume). This coil has a huge problem in
a field inhomogeneity resulting in strong occipital hypersignal and frontal
hyposignal, from which I believe all my problems originate.
- The standard pipeline provide an incomplete temporal and frontal
segmentation (white and pial surfaces do not include enough) while over
including in occipital and parietal.
- We tried using the watershed 40 value from the skulltrip to get more of
the occipital (we had a few subjects having holes in occipital within the
brain segmentation). This option changed also the segmentation resulting in
better segmentation for temporal and frontal but worse in parietal and
occipital.
- We tried control points as well, without success (as you can imagine due
to the fronto-occipital inhomogeneity). We also tried manually removing
extra voxels from the white surface to correct it. But unfortunately, this
is not an option because we have about 200 scans to process.
- We tried using N4 intensity bias correction on the raw images before
feeding it to freesurfer, but the segmentation did not run through for all
participants (stuck in fixing topology for more than a week) and for those
working, the pial surface did not include enough grey matter.
I am now thinking about playing with the option of intensity normalization
(mri_ca_normalize) within freesurfer but would like to have your expert
opinion on that before roaming. Any advice on how to set up mri_ca_normalize
to retrieve a good white matter homogeneity? Or any other functions I should
be playing around with?
Thanks a lot in advance for your help,
Kind regards,
Élodie
Élodie CAUVET | PhD
Karolinska Institutet Center of Neurodevelopmental Disorders
(KIND)
Gävlegatan 22B, floor 8 | 113 30 Stockholm
+46 (0)8 514 527 10 | +46 (0)728 774 058
elodie.cau...@ki.se
http://ki.se/en/kind/startpage
http://elodiecauvet.wordpress.com/
Karolinska Institutet – a medical university
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