Hi Ryu,
do you have any freedom to modify the acquisition? Not sure why things are crashing, but the image is pretty low quality, both in terms of distortions and in contrast. If you give us the details and constraints on your imaging we can make some suggestions.
Also, can you send us the full output of recon-all?
cheers, Bruce
On Fri, 27 Jan 2006, Ryu-Ichiro Hashimoto wrote:
Dear all,
I am trying "RecommendedReconstruction", following Wiki instruction. My problem is, after the first step of recon-all ("recon-all -autorecon1") when I try to check the talairach transform (by tkregister2 --mgz ... --fstal), I get an image incorrectly aligned ... image is displayed in quadrant (pls see ac_aft_reconall1_target.jpg). In this display, I cannot manually adjust it for coregistration. When I continue to run autorecon2, it crashes.
For checking skull strip, it is correctly displayed (ac_aft_reconall1_tkmedit.jpg).
I thought problem could be already present in converting from dicom to mgz, as there seems to be some missing info (message_conv.txt), though I am not sure whether it is really relevant. The image was obtained by 3T GE magnet with SPGR at BWH.
Any thoughts regarding above are greatly appreciated.
Thanks in advance for your help.
Ryu Hashimoto