Dear Freesurfer list,
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 elodiehttps://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnpzYcDGssK3pRtytCgUbLpGEkOSfWZru4jXZIc4.&URL=https%3a%2f%2femail.ki.se%2fowa%2fredir.aspx%3fC%3dO04EzIBOBESdqb5UF4tQ2ZaT42_b8c8IiuN1kTLIqXFqzw13jsfS72Um0eIyNBZzcZeYuUfj3nw.%26URL%3dmailto%253aelodie.cauvet%2540ki.se.cauvet@ki.sehttps://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnpzYcDGssK3pRtytCgUbLpGEkOSfWZru4jXZIc4.&URL=https%3a%2f%2femail.ki.se%2fowa%2fredir.aspx%3fC%3dO04EzIBOBESdqb5UF4tQ2ZaT42_b8c8IiuN1kTLIqXFqzw13jsfS72Um0eIyNBZzcZeYuUfj3nw.%26URL%3dmailto%253aelodie.cauvet%2540ki.se http://ki.se/en/kind/startpagehttps://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnpzYcDGssK3pRtytCgUbLpGEkOSfWZru4jXZIc4.&URL=http%3a%2f%2fki.se%2fen%2fkind%2fstartpage http://elodiecauvet.wordpress.com/https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnpzYcDGssK3pRtytCgUbLpGEkOSfWZru4jXZIc4.&URL=http%3a%2f%2felodiecauvet.wordpress.com%2f Karolinska Institutet – a medical university