Different standard space for SSwarper

AFNI Message Board
1

Hi AFNI team!

I'm planning to begin preprocessing with SSwarper and would like to use the mni_icbm152_nlin_asym_09c template as a standard space. This is for comparison of the upcoming results with previous outcomes obtained from fMRIPrep. Upon searching, it appears that this particular template is not included in AFNI's default set. I assume I need to integrate it manually. Could you guide me on how to modify the template variable accordingly? Below, I've attached a segment of the code for reference. Thank you in advance for your assistance!

Byeol from Dartmouth

AFNI version info (afni -ver): 23.0.04

set template       = MNI152_2009_template_SSW.nii.gz 
...

time @SSwarper                                                        \
    -base    "${template}"                                            \
    -subid   "${subj}"                                                \
    -input   "${dset_anat_00}"                                        \
    -odir    "${sdir_ssw}"
2

Hello, Byeol of Dartmouth!

Actually, the MNI152_2009_template_SSW.nii.gz dataset is the mni_icbm152_t1_tal_nlin_asym_09c one (here is the [0]th volume of the former displayed over the latter):

Screenshot from 2023-12-18 16-05-45
Screenshot from 2023-12-18 16-05-451027×387 185 KB

... and they even have the same grid:

$ 3dinfo \
    -same_all_grid \
    mni_icbm152_t1_tal_nlin_asym_09c.nii \
    MNI152_2009_template_SSW.nii.gz 
1	1	1	1	1
1	1	1	1	1

I'll just note for reference that a description of what makes the *SSW* templates specific to the actions of @SSwarper is here. Namely, the multiple volumes in that *SSW* version are useful for the combined skullstripping and warping.

Note that the datum type of the *SSW* version is short, while the mni*nii one there is float datum. Also, note that the *SSW* has been "sharpened" with 3dSharpen to slightly improve better gray-white tissue contrast.

The MNI152_2009_template.nii.gz is the simple, single brick version of that dataset, actually, which we distribute, too.

--pt

1 Like
3

Hi Paul,

Good to see you here! I was wondering which MNI version of MNI152_2009_template_SSW.nii and I will use it then.
Thank you so much for clarifying these!

Byeol

4

Sure thing, makes sense to ask. We should probably stick a note in the history of the file and on the SSW template page, to help clarify.

--pt

5

And actually, one last point to add here for anyone in the future asking about expanding the list of SSW target volumes: it is certainly possible to create further targets, and we are happy to help with it whenever the need arises. This reference page explicitly has scripts for helping to build one from existing templates, as exemplars of this process.

--pt

1 Like