The freesurfer results are going to be in the anatomical space (256^3, 1mm^3). Your functional results will be in a different space (eg, 64x64x30 or whatever), so you'll need to put the functionals into the anatomical space or the other way around. You'll need a registration matrix between the two (you can use bbregister), then use mri_vol2vol to put the functionals into anatomical space or mri_label2vol to put the segmentations into functional space.

doug

Wu, Paula (NIH/NIMH) [F] wrote:

Hello,

I am trying to create white matter, grey matter, and CSF masks (along with some other finer segmentations) using Freesurfer, and then use these to find the average BOLD response for all voxels within each mask using AFNI’s 3dmaskave.

So far, I have performed the following steps.

-Talairach-aligned the T1 using @auto_tlrc in AFNI

/@auto_tlrc -base TT_N27+tlrc -input mprage_scan_3+orig /

-ran recon-all –notalairach using this T1

/recon-all –s 09_07_23_DM –all –notalairach /

-created the masks using mri_convert and 3dcalc. For example,

/mri_convert -it mgz -ot nii -i aseg.mgz -o aseg.nii /

/3dcalc -a aseg.nii -expr 'equals(a,4) +equals(a,43) +equals(a,14) +equals(a,15) +equals(a,5) +equals(a,44)' -prefix mask_ventricles_all /

I am now attempting ot use 3dmaskave to pull out the average response from talairach aligned trial averages, but I get the error that the input (trial averages – preprocessing and deconvolution done in AFNI) and mask datasets are not the same dimensions.

E.g. /3dmaskave -mask [nameoffile]+orig -quiet s04_trialavg_dt_st_reg_20mmHg20s_10sshifted_al+tlrc > mask_{$roi}_$condition.1D.txt /

Any suggestions?

Paula

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