I am trying to register my T2 images to the template and I am using the following command (I would like to skip step 2 and run the registration with default parameters of steps 0 and 1- this is why I manually define all the parameters).
type=label does not refer to disc labels, but to points which are used as a coarse pre-registration (e.g., to bring source image into destination image). This could be useful in case the two physical coordinate system are different your image to the template space, e.g., in case of subject repositioning between source and destination. When using this option, you need to provide your labels with the flags -ilabel and -dlabel.
In the case of registration to template, step=0 is dealt with internally using the provided discs, so you should not interfere with step=0.
if you want to remove step=2 (or add more steps), you can simply omit step=0 in the syntax, and by default it will use the disc labels for step=0. So, the syntax would look like:
Thank you very much for your reply and for the explanation.
Unfortunately, I encounter another problem right now. So I just copied the line you have sent and tried to run it.
Then I got the following error:
Folder RegsTmpSmooth_woStep2 has been created.
Please check parameter -param (usage changed from previous version)
Traceback (most recent call last):
File "/home/raid2/mkaptan/sct_4.0.2/scripts/sct_register_to_template.py", line 871, in <module>
main()
File "/home/raid2/mkaptan/sct_4.0.2/scripts/sct_register_to_template.py", line 233, in main
paramreg.addStep(paramStep)
File "/home/raid2/mkaptan/sct_4.0.2/scripts/sct_register_multimodal.py", line 279, in addStep
param_reg.update(stepParam)
File "/home/raid2/mkaptan/sct_4.0.2/scripts/sct_register_multimodal.py", line 259, in update
setattr(self, obj[0], obj[1])
IndexError: list index out of range