Transcription of FreeSurfer
1 FreeSurfer Alex / 2020-04-18 / FreeSurfer T1 ROI FreeSurfer FreeSurfer Wiki parcellation 4 FreeSurfer recon-all FreeSurfer DK Atlas thickness stats DK Atlas :aparcstats2table --subjects sub001 --hemi lh --meas thickness --skip --subjects / --hemi --meas --tablefile FreeSurfer FreeSurfer lGI lGI recon-all -s sub001 -localGI SUBJECTS_DIR lGI mris_anatomical_stats -a ${SUBJECTS_DIR}/sub001/ -t pial_lgi-f ${SUBJECTS_DIR}/sub001/ sub001 lh lGI.
2 Aparcstats2table --subjects sub001 --hemi lh --meas thickness --skip --parc aparc_lgi --tablefile --meas thickness lGI Yeo Atlas Yeo Atlas fsaverage native :mri_surf2surf --srcsubject fsaverage --trgsubject sub001 --hemi lh --sval-annot ${FREESURFER_HOME}/subjects/fsaverage/ --tval ${SUBJECTS_DIR}/sub001/ Yeo Atlas mris_anatomical_stats -a ${SUBJECTS_DIR}/sub001/ -f ${SUBJECTS_DIR}/sub001/ sub001 lh aparcstats2table --subjects sub001 --hemi lh --meas thickness --skip --parc Yeo2011_7 Networks_N1000 --tablefile (gca/gcs)
3 Brainnetome Atlas, BN fsaverage native BN Atlas BN Atlas fsaverage native mris_ca_label -l ${SUBJECTS_DIR}/sub001/ sub001 lh ${SUBJECTS_DIR}/sub001/ ${BN_Atlas} ${SUBJECTS_DIR}/sub001/ ${BN_Atlas} BN Atlas BN Atlas mris_anatomical_stats -mgz -cortex ${SUBJECTS_DIR}/sub001/ -f ${SUBJECTS_DIR}/sub001/ -b -a ${SUBJECTS_DIR}/sub001/ -c ${BN_Atlas} sub001 lh white aparcstats2table --subjects sub001 --hemi lh --parc BN_Atlas --meas thickness --tablefile FreeSurfer mean curvature
4 Gaussian curvature intrisinc curvature index folding index sulcal depth local gyrification index surf recon-all surf ? white surface ? pial surface ? inflated surface ? ? * k1/k2/K/H/C/S/BE/SI/FI ? ? ? sulcal depth Hill et al., 2010 lGI lGI mris_curvature mris_curvature_stats : mris_curvature_stats --writeCurvatureFiles -G -F inflated sub001 lh stats recon-all stats ROI MeanCurv GausCurv mris_anatomical_stats mris_curvature_stats ROI ROI ROI DK Atlas 34 Matlab [thickness, fnum ]=read_curv('/home/alex/ FreeSurfer /subje cts/fsaverage/ ').
5 %% [vertices, label, colortable] = read_annotation('/home/alex/ FreeSurfer /s ubjects/fsaverage/ '); %% label colortable 36 stats = xlsread('/home/ '); %% 34*1 stats = [0; stats(1:3); 0; stats(4:34)]; %% 1 5 unknown corpuscallosum 0 lh_stats = zeros(size(lh_thickness));for i = 1:length( ) idx = label == (i,5); lh_stats(idx) = stats(i);end %% vertexwrite_curv('/home/ ', lh_stats, fnum); %% freeview longitudinal design recon-all -all -s TP1 -i -all -s TP2 -i T1 $SUBJECTS_DIR recon-all -all -base Base -tp TP1 -tp TP2 Base recon-all -all -long TP1 Baserecon-all -all -long TP2 Base FreeSurfer native space FreeSurfer recon-all 1mm/256*256*256 comformed space
6 Mri_label2vol --seg --temp --o --regheader mask mask mri_extract_label 17 53 FreeSurfer FreeSurfer FreeSurfer export SUBJECTS_DIR=${T1 DIR}recon-all -i ${T1 FILE} -s FreeSurfer -autorecon1 -noskullstripmri_mask ${T1 DIR}/ FreeSurfer / ${T1 DIR} ${T1 DIR}/ FreeSurfer / -s FreeSurfer -autorecon2 -autorecon3 -autorecon1 -noskullstrip FreeSurfer -autorecon2 -autorecon3 T1 mri_robust_template nii mgzmri_convert --in_type nii --in_type nii mri_robust_template mri_robust_template --mov *.
7 Mgz --template --satit mgz niimri_convert --in_type mgz mri_robust_template 1mm Van Essen, D. C., and H. A. Drury. "Structural and functional analyses of human cerebral cortex using a surface-based atlas." Journal of Neuroscience (1997): 7079-7102. Shimony, Joshua S., et al. "Comparison of cortical folding measures for evaluation of developing human brain." Neuroimage 125 (2016): 780-790. Hill, Jason, et al. "A surface-based analysis of hemispheric asymmetries and folding of cerebral cortex in term-born human infants.
8 " Journal of Neuroscience (2010): 2268-2276.
