Hi all,
I have two problems here.
1. talairach.xfm By browsing through the mailing list, it seems that talairach.xfm was not used much in the recon-all process which is quite different from the table given at https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps. We did find many subjects with bad talairach transformation but reasonable segmentation and surface reconstruction (version 3.05). Are the results (volumes and cortical thickness) for those subjects still trustworthy? Can you kindly clarify the importance of talairach.xfm in the pipeline? And since the new method of eTIV uses this transformation, is there any way to ensure manual registration is fine enough to be used for this estimation, if I have to manually register those subjects mentioned above?
2. recon-all -long We processed our data with the longitudinal pipeline. So far we only found 6 subjects failed among 200 subjects (tp1 corrected). All these 6 subjects seemed to have problem during the registration from tp2 to tp1. I used the command "tkmedit -f tp2.long.tp1/mri/orig.mgz -aux tp2.long.tp1/mri/orig_tp1_to_tp2.long.tp1.mgz" and realized they were not aligned. I have tried different cost functions using "fsl_rigid_registration". All of them gave the same result. Is there any way I can do the manual registration? I used "fsl_rigid_registration" because no matter which cost function I specified to recon-all -long, it would call "fsl_rigid_registration" with corratio as the cost function.
Thanks in advance, Zheng Hui