Hi afni group:

I had two ways to do group analysis in my mind.

The first is based on the volume data, just simply @auto_tlrc the first level glts file for each participant and do anova (in my case, 3dMVM).

The second is based on the surface data. 1) do 3dVol2Surf on the first level glts file of each participant, 2) with the surface data (1d file) do the same anova, 3), do 3dSurf2Vol to transform the surface data back to volume data.

I assumed those two ways might have slightly different values but the same pattern. While when I checked the results from two methods, they did show a very similar contrast pattern, but the statistical value range differ a lot. The activation from surface data were more robust ( a lot).

Here is the codes that I used just in case you want to check the detail.

method 1:

@auto_tlrc -apar Anatomical_reg_norm+tlrc -input GLM_glts+orig -dxyz 3 -rmode NN -suffix _at

3dMVM

3dMVM -prefix $spath/group/group_MVM -jobs 4 \
			-bsVars 'Modality' \
			-wsVars 'Scale' \
			-SS_type 2 \
			-num_glt 25 \
			-mask "$spath"/group/mask_group+tlrc \
			-gltLabel 1 Listen_NS -gltCode 1 'Modality : 1*Listen Scale : 1*NS' \
		
		...
		            -gltLabel 24 US_ Read-Listen -gltCode 24 'Scale : 1*US Modality : 1*Read -1*Listen' \
                         -gltLabel 25 SW_ Read-Listen -gltCode 25 'Scale : 1*SW Modality : 1*Read -1*Listen' \
			-dataTable \ 
			Subj	Modality	Scale	InputFile \
			s2	Listen	NS	"$spath"/sub02/orig_files/GLM_glts_at+tlrc'[6]' \
			s2	Listen	CS	"$spath"/sub02/orig_files/GLM_glts_at+tlrc'[0]' \
			...
                        ...
			s9	Listen	CS	"$spath"/sub09/orig_files/GLM_glts_at+tlrc'[0]' \
			s9	Listen	US	"$spath"/sub09/orig_files/GLM_glts_at+tlrc'[2]' \
			s9	Listen	SW	"$spath"/sub09/orig_files/GLM_glts_at+tlrc'[4]' \

method 2:
3dVol2Surf

cd "$spath"/"$sub"/orig_files/
	set infile = GLM_glts

	foreach hemi(lh rh)
		echo "Working on: $infile -->  $hemi ... "
		rm ../surface_files/"$hemi"_"$infile".1D
	
		3dVol2Surf \
			-spec ../freesurfer/SUMA/std."$sub"_"$hemi".spec \
			-surf_A smoothwm \
			-surf_B pial \
			-sv Anatomical_reg_AlndExp+orig \
			-grid_parent "$infile"+orig \
			-map_func max_abs \
			-f_steps 15 \
			-f_index voxels \
			-oob_value 0 \
			-no_headers \
			-out_1D ../surface_files/"$hemi"_"$infile".1D
	end

foreach hemi(lh rh)

	3dMVM -prefix "$hemi"_group_MVM -jobs 12 \
			-bsVars 'Modality' \
			-wsVars 'Scale' \
			-SS_type 2 \
			-num_glt 25 \
			-gltLabel 1 Listen_NS -gltCode 1 'Modality : 1*Listen Scale : 1*NS' \
			-gltLabel 2 Listen_CS -gltCode 2 'Modality : 1*Listen Scale : 1*CS' \
	...
        ...
            -gltLabel 24 US_ Read-Listen -gltCode 24 'Scale : 1*US Modality : 1*Read -1*Listen' \
            -gltLabel 25 SW_ Read-Listen -gltCode 25 'Scale : 1*SW Modality : 1*Read -1*Listen' \
			-dataTable \
			Subj	Modality	Scale	InputFile \
			s2	Listen	NS	"$spath"/sub02/surface_files/"$hemi"_GLM_glts.1D'[12]' \
			s2	Listen	CS	"$spath"/sub02/surface_files/"$hemi"_GLM_glts.1D'[6]' \
			...
			s7	Listen	CS	"$spath"/sub07/surface_files/"$hemi"_GLM_glts.1D'[6]' \

after 3dMVM, transform the surface results to volume data

#provide an index column for the results for 3dSurf2Vol
foreach hemi(lh rh)
	1dcat "$spath"/sub02/surface_files/"$hemi"_GLM_glts.1D'[0]' \
		"$hemi"_group_MVM.1D \
		>> "$hemi"_group_MVM.dset
end
#put group results back into volume world
foreach hemi(lh rh)
#			rm "$hemi"_group_MVM.dset
			3dSurf2Vol \
				-spec "$spath"/group/freesurfer/SUMA/subAvg_"$hemi"+tlrc.spec \
				-surf_A smoothwm \
				-surf_B pial \
				-sv ../subAvg_SurfVol_at+tlrc.nii.gz \
				-grid_parent "$spath"/sub02/orig_files/GLM_glts_at+tlrc. \
				-sdata_1D "$hemi"_group_MVM.dset \
				-datum float \
				-map_func max_abs \
				-f_steps 15 \
				-f_index voxels \
				-f_p1_fr -0.2 -f_pn_fr 0.4 \
				-prefix ./"$hemi"_group_MVM
end
rm group_MVM.nii.gz
3dcalc \
	-float \
	-a lh_group_MVM+tlrc. \
	-b rh_group_MVM+tlrc. \
	-expr '(a+b)' \
	-prefix group_MVM.nii.gz

The below links show the two renderings
from surface data
[drive.google.com]

from volume data
[drive.google.com]

They were rendering with the same threshold and cluster size.

Thank you so much!!!

Meng



Edited 2 time(s). Last edit at 02/20/2019 04:00AM by Liu Mengxing.