Running into @SSWarper error

Dear expert,
I am running @SSWarper on a new machine to get the transformation from the T1 subject space to the MNI. Here the command that I am running:

@SSwarper -input T1.nii -base MNI152_2009_template_SSW.nii.gz -subid sub006

I get the following error right after the first pass of skull stripping:

  • ERROR: Totally bogus option ‘-awarp’
    Here’s hoping these excerpts from ‘3dQwarp -help’ enlighten:
    ‘-plusminus = Normally, the warp displacements dis(x) are defined to match’
    ‘-ballopt = Normally, the incremental warp parameters are optimized inside’
    ‘-noXdis = These options let you specify that the warp should not’
    ++ no -frac option: defaulting to -union
    ++ processing 1 input datasets…
    ++ padding all datasets by 1 (for dilations)
    ++ frac 0 over 1 volumes gives min count 0
    ++ voxel limits: 0 clipped, 2000189 survived, 6529832 were zero
    ++ writing result junk.SSwarper.bdcqBmkqmvW_MASK.nii…
    ++ Output dataset ./junk.SSwarper.bdcqBmkqmvW_MASK.nii
    ++ 3dcalc: AFNI version=AFNI_16.2.16 (Sep 4 2016) [64-bit]
    ++ Authored by: A cast of thousands
    ** ERROR (nifti_image_read): failed to find header file for ‘./junk.SSwarper.bdcqBmkqmvW_TAL5.nii’
    ** FATAL ERROR: can’t open dataset ./junk.SSwarper.bdcqBmkqmvW_TAL5.nii

Any help would be appreciated.


Ciao, Giovanni-

What is your AFNI version number + system you are running on? I just tried that @SSwarper command on two different computers here (with one of the Bootcamp dset anatomical vols), and nothing bad like that happened.

And if you look at any of the output intermediate datasets, is something obviously wrong with any?


Hi Giovanni,

Paul is right, that output shows AFNI version “AFNI_16.2.16 (Sep 4 2016)”, but Bob added that 3dQwarp option in December of 2016.

Maybe you are ready for an update?

  • rick

Dear all,

thank you for your message. Actually, I had been told that the PC had the new version of AFNI but I did not realize that the .bashrc was still pointing to the old version; my bad…