Hi Mark,
I did some pos tprocessing and I think I have problem again in this step. So I
came back to this question. I checked the scripts of run_first_all and
first_flirt. It seems that the matrix is the concatened matrix of registration in
stage 1 and stage2. So, you mean that I should use only mat_stage1.mat or
only mat_stage2.mat or -concat <mat_stage1.mat>, <mat_stag2.mat>?
I have another question that may be related to above again. FSL does the
segmentation on images that their dimention and orientation is not necessary
the same as MNI152_T1_1mm. The dimention and orientation of the first and
second steps of registration change to MNI reference image as I checked in
first_flirt (by debugging), but the final segmented image has the same
orientation and dimention of the original image. I tracked the scripts
run_first_all, first_flirt and run_first. I didn't find any step that this resampling
to original grid and orientation occurs. Could you please guide me in this
regard?
Siamak
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