Skull Stripping in AFNI

AFNI version info (afni -ver): 24.1

Hello Afni Gurus!

Our lab uses to preprocess ME data. We use an MP2RAGE sequence for registration.
Our Pipeline is comprised of the following general steps -
(1) Dicom to AFNI
(2) Creating an anatomical mask using the INV2 series acquired during MP2RAGE, and using that mask for skull stripping:

  • 3dUnifize with INV2 as an input
  • 3dWarp -deoblique with both INV2 and the unified series from MP2RAGE
  • 3dresample post deobliquing
  • 3dskullstrip post 3dresample --> creating SSanat2
  • 3dAutomask --> 3dcalc to create mask

I'm attaching this bit of code here for clarity -

#### correction for the inhomogeneity of the field to file anat2
3dUnifize -prefix ${subject}.7TMS.${session}.anat2.uni $path_session/'anat2'/${subject}.7TMS.${session}.anat2+orig.

#### Deoblique for files anat 2 (corrected) and anat
3dWarp -deoblique -prefix ${subject}.7TMS.${session}.anat2.Deobl ${subject}.7TMS.${session}.anat2.uni+orig

3dWarp -deoblique -prefix ${subject}.7TMS.${session}.anat.Deobl $path_session/'anat'/${subject}.7TMS.${session}.anat+orig.

#### correct the orientation (that is changed when deoblique)
3dresample -orient ASR -rmode NN -prefix ${subject}.7TMS.${session}.anat2.DeoblASR -input ${subject}.7TMS.${session}.anat2.Deobl+orig.

3dresample -orient ASR -rmode NN -prefix ${subject}.7TMS.${session}.anat.DeoblASR -input ${subject}.7TMS.${session}.anat.Deobl+orig.
#### 3dskullstrip for anat2 and create mask

3dSkullStrip -input ${subject}.7TMS.${session}.anat2.DeoblASR+orig -prefix SSanat2

3dAutomask -prefix Automask SSanat2+orig 

#### create anat mask out of the automask
3dcalc -a Automask+orig -b ${subject}.7TMS.${session}.anat.DeoblASR+orig -expr 'a*b' -prefix ${subject}.7TMS.${session}.anatMASK

Following these steps we use We use SSwarper to create the inputs requires in order to run (anatQQ/SS). As input, SSwarper receives the final product of the bit of code pasted above - which is a skull-stripped MP2RAGE image. We are aware of the fact that SSwarper requires a non-skull stripped input, but unfortunately it isn't doing a good job with stripping our original MP2RAGE image :(.
This is the bit of code that follows -

cd $path

for file in anatQQ.*; do
    if [[ -f $file ]]; then
    	echo 'anat.QQ FILES exsist'
        echo 'preforming @SSwraper'
        export OMP_NUM_THREADS 4
        @SSwarper                                                                      \
		   -input  $subject.$experiment.$session.anatMASK+orig.BRIK                       \
		   -base   $abin_path/MNI152_2009_template_SSW.nii.gz                                  \
		   -subid  $subject.$experiment.$session

for scan in ${scans[@]}

echo "preforming to scan $scan" \
     -subj_id $subject.$experiment.$session.$scan \
     -out_dir ${output_path}/$subject.$experiment.$session.$scan.results \
     -script ${output_path}/proc.$subject.$experiment.$session.$scan \
     -blocks despike tshift align tlrc volreg mask combine scale regress \
     -radial_correlate_blocks tcat volreg                      \
     -blip_forward_dset $subject.$experiment.$session.AP+orig.HEAD -align_unifize_epi local \
     -blip_reverse_dset $subject.$experiment.$session.PA+orig.HEAD                     \
     -copy_anat anatSS.$subject.$experiment.$session.nii \
     -anat_has_skull no \
     -dsets_me_run $subject.$experiment.$session.${scan}*0?+orig.HEAD \
     -echo_times 13.2 34.72 56.24 \
     -reg_echo 1                                               \
     -tcat_remove_first_trs 4                                  \
     -tshift_interp -wsinc9                                    \
     -align_opts_aea -cost lpc+ZZ -check_flip            \
     -tlrc_base MNI152_2009_template_SSW.nii.gz               \
     -tlrc_NL_warp                                             \
     -tlrc_NL_warped_dsets anatQQ.$subject.$experiment.$session.nii anatQQ.$subject.$experiment.$session.aff12.1D anatQQ.$subject.$experiment.${session}_WARP.nii \
     -volreg_align_to MIN_OUTLIER                              \
     -volreg_align_e2a                                         \
     -volreg_tlrc_warp                                         \
     -mask_epi_anat yes                                        \
     -mask_apply anat \
     -combine_method m_tedana                                    \
     -html_review_style pythonic \

tcsh -xef $output_path/proc.$subject.$experiment.$session.$scan 2>&1 | tee $output_path/output.proc.$subject.$experiment.$session.$scan

## copy final output to shared folder
echo "copying final errts and anat files to shared folder: $shared_output"

cp ${output_path}/$subject.$experiment.$session.$scan.results/errts* $shared_output


cp ${output_path}/$subject.$experiment.$session.$scan.results/anat_final* $shared_output/anat_final.$subject.$experiment.$session


The problem is that no matter what options we try, SSwarper (and also SSwarper2) sometimes takes a bite out of the skull stripped input it receives, taking out part of the cortex / cerebellum.
For instance -

Any suggestions on how we can work this out? We have a method for skull stripping without SSwarper. We want to move to MNI, and use that product with, but to avoid skull stripping any further.

  1. Is there a way to add a flag to SSwarper to prevent it from Skull Stripping, and just warping to MNI?
  2. Any way creating the files needs without using SSwarper?

Thank you in advance!!!!!


If you already have a skullstripped anatomical, then you could just use 3dQwarp directly, instead of @SSwarper or sswarper. Those latter programs are wrappers for 3dQwarp, and they do work assuming that they need to pair skull removal with alignment. It wouldn't surprise me that results might be a bit odd sometimes if the properties of the inputs are changed notably, as here.

There are a couple different ways to do it---call 3dAllineate before 3dQwarp, or just use the latter with the -allineate option. In the end, to provide the pre-calculated warp to, you still need to provide 3 datasets: the warped dataset in template space; the affine part of the alignment (*aff12.1D file); and the nonlinear part of the warp (*_WARP* dset).

I would recommend perhaps starting with this, which will assume that your initial skullstripping is good, and we'll use the same *SSW* reference template base that has multiple bricks:

set Basedset = MNI152_2009_template_SSW.nii.gz

 3dQwarp        \
        -allineate \
        -allineate_opts "-twopass -cmass" \
        -base     "${Basedset}[0]"            \
        -source   DSET_IN    \
        -lpa                           \
        -pblur 0 1 \
        -weight "${Basedset}[2]"              \
        -inedge                  \
        -prefix DSET_OUT.nii

Your input anatomical is DSET_IN, and the result aligned to the template will be DSET_OUT.nii, while there will also be a DSET_OUT_WARP.nii.

NB: There will be an *.aff12.1D matrix file also output, but that that file is just intermediate and it shouldn't be used with the warp here when passed to It can be a little confusing, but when 3dQwarp does an initial affine estimate, it will already include that information in the output *_WARP* dset; but when @SSwarper or sswarper2 uses affine early on, it does not include it directly in the warp, so both have to be given. Therefore, in this scenario, we have to hand a placeholder identity matrix file in the set of 3 inputs. You can make one called mat_identity.aff12.1D whose contents are just this (I put spaces to break up the quartets visually):

1 0 0 0   0 1 0 0   0 0 1 0

Then, if alignment is good, you can provide the results to like:

 -tlrc_NL_warped_dsets  DSET_OUT.nii      \
       mat_identity.aff12.1D   \
        DSET_OUT_WARP.nii   \

How does that sound?


If the input anatomical dataset, then you should provide this option (same as before):

           -anat_has_skull           no                                  \

If there are no warps provided, then will call to do the affine and nonlinear alignment to a template. calls @auto_tlrc and 3dQwarp. It's a bit different than the 3dQwarp-allineate method because @auto_tlrc uses 3dWarpDrive by default and not 3dAllineate for its affine alignment. For, you would still need to provide a template, of course, along with the option to do the nonlinear warping and be sure to include the tlrc block in the processing blocks.

           ... \
           -tlrc_base   MNI152_2009_template.nii.gz   \
           -tlrc_NL_warp   \

In the end, there are fewer options for because you won't provide the warp and the affine transformation.