Good Afternoon,

I am attempting to get a list of cortical thickness statistics on a group of ROIs. The T2 functional data for the subjects was previously analyzed in AFNI, where an ROI mask to be applied to all subjects, was developed. The volume ROI mask was converted from AFNI BRIK to FreeSurfer .mgz format using mri_convert. Recon-all has been run on all T1 anatomical images and fslregister was used to register each subject's anatomical data to the ROI mask. I ran the series of commands below and got results, but the anatomical locations and Talairaich coordinates from FreeSurfer are not close to the values I see in AFNI.

How and when should I be aligning the center and orientation of the average subject with the functional mask from AFNI?

Here is what I tried, but still did not get accurate results even when mris_info shows the same for both the anatomy and functional mask image files:

#

cd $SUBJECTS_DIR/MSN.0964.anat/mri

mri_convert --apply_transform transforms/talairach.xfm --conform --devolvexfm MSN.0964.anat -ic 0 0 0 orig.mgz orig_Talc000.mgz

mri_convert --like orig_Talc000.mgz --conform --devolvexfm MSN.0964.anat -ic 0 0 0 OR_MASK_0005_clust_400_contiguous+tlrc.mgz OR_MASK_Talc000.mgz

#

mri_info orig_Talc000.mgz >mri_info.orig_Talc000.mgz

mri_info OR_MASK_Talc000.mgz > mri_info.OR_MASK_Talc000.mgz

#

#Using the group ROI mask as a volume dataset in FreeSurfer, I ran the following commands:

#

# Create average subject

cd $SUBJECTS_DIR

make_average_subject --out MSNaverage --subjects MSN.0964.anat MSN.0965.anat MSN.0966.anat MSN.0967.anat MSN.0968.anat MSN.0969.anat MSN.0979.anat MSN.0980.anat MSN.1001.anat MSN.1003.anat MSN.1039.anat

#

# Register functional map to average subject.

fslregister --mov $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --s MSNaverage --reg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat

#

# Convert functional mask from AFNI to a surface (both volume and surface belong to the average subject

mri_vol2surf --src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \

--hemi lh --fwhm 6 --out_type mgz --o $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz --trgsubject MSNaverage --nvox $SUBJECTS_DIR/MSNaverage/stats/lh.nvox.dat

mri_vol2surf --src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \

--hemi rh --fwhm 6 --out_type mgz --o $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz --trgsubject MSNaverage --nvox $SUBJECTS_DIR/MSNaverage/stats/rh.nvox.dat

#

# Map average subject surface to subject MSN.0964.anat surface

mri_surf2surf --srcsubject MSNaverage --srcsurfval $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz \

--trgsubject MSN.0964.anat --trgsurfval $SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi lh

mri_surf2surf --srcsubject MSNaverage --srcsurfval $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz \

--trgsubject MSN.0964.anat --trgsurfval $SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi rh

#

#Create a surface cluster & label for each ROI for subject MSN.0964.anat

#generates region & fixed mni (mni2tal.mat) coordinates for each ROI

mri_surfcluster --in $SUBJECTS_DIR/MSN.0964.anat/surf/lh.fvol2pialsurf.mgz --subject MSN.0964.anat --hemi lh --annot aparc --thmin 1 --thmax 11 --minarea .01 \

--fixmni --olab lh.pial.surf --sum $SUBJECTS_DIR/MSN.0964.anat/stats/lh.pial.sum.MSN.0964.anat.txt --o lh.pial.clustsurf --ocn lh.vertex.pial.ClusterNum

mri_surfcluster --in $SUBJECTS_DIR/MSN.0964.anat/surf/rh.fvol2pialsurf.mgz --subject MSN.0964.anat --hemi rh --annot aparc --thmin 1 --thmax 11 --minarea .01 \

--fixmni --olab rh.pial.surf --sum $SUBJECTS_DIR/MSN.0964.anat/stats/rh.pial.sum.MSN.0964.anat.txt --o rh.pial.clustsurf --ocn rh.vertex.pial.ClusterNum

#

# Generate statistics for each ROI for each subject

set left_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 )

set right_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 )

foreach right_roi ( $right_rois )

mri_label2label --srcsubject MSNaverage --srclabel $SUBJECTS_DIR/MSNaverage/label/rh.pial.surf-00${right_roi}.label --trgsubject MSN.0964.anat --trglabel $SUBJECTS_DIR/MSN.0964.anat/label/rh.pial.surf-00${right_roi}.label --regmethod surface --hemi rh

mris_anatomical_stats -l rh.pial.surf-00${right_roi}.label -f $SUBJECTS_DIR/MSN.0964.anat/stats/rh.ROI${right_roi}.pial.surfstats -b MSN.0964.anat rh white

end

foreach left_roi ( $left_rois )

mri_label2label --srcsubject MSNaverage --srclabel $SUBJECTS_DIR/MSNaverage/label/lh.pial.surf-00${right_roi}.label --trgsubject MSN.0964.anat --trglabel $SUBJECTS_DIR/MSN.0964.anat/label/lh.pial.surf-00${right_roi}.label --regmethod surface --hemi lh

mris_anatomical_stats -l lh.pial.surf-00${left_roi}.label -f $SUBJECTS_DIR/MSN.0964.anat/stats/lh.ROI${left_roi}.pial.surfstats -b MSN.0964.anat lh white

end#

Any insight on this process would be greatly appreciated.

Thanks very much for your help.

Denise M. Cote

Sr. Research Assistant

Transdisciplinary Research Group

Butler Hospital

345 Blackstone Blvd

Providence, RI