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May 10, 2022 05:45PM
Hi, Philipp-

Hmm, I am not sure what the issue here is. Could you please run your same command above but also include "-echo" as an option, and then dump a copy of the terminal output to a text file, too. If you are using bash/zsh, this would be done as:
@SSwarper -input anat+orig. -base MNI2009_to_MNI+tlrc.BRIK -subid sswarp_anat2mni \
    -echo \
    2>&1 | tee o.ssw.txt
... and if you are using tcsh/csh, this would be done as:
@SSwarper -input anat+orig. -base MNI2009_to_MNI+tlrc.BRIK -subid sswarp_anat2mni \
    -echo \
   |& tee o.ssw.txt
Then could you please email me the o.ssw.txt text, so I can check it. (If you click on my username in the MB interface here, you will see my email.)

Separately (or perhaps related... but this should not be the cause of your error above) but importantly, when running @SSwarper, you should use only one of the available SSW reference sets as a base:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/%40SSwarper_sphx.html#reference-datasets
These are special versions of known templates, because they have multiple volumes. So, probably you should be running with:
-base MNI152_2009_template_SSW.nii.gz
But let's troubleshoot the first issue first.

thanks,
pt
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