#!/bin/csh -f ##TO RUN THIS SCRIPT, TYPE IN THE NAME OF THE SUBJECT YOU WANT TO RUN AFTER THE SCRIPT'S NAME: ex. 'fs_roi_2_afni.s {$subj}' ##Make sure thalamic ROIs are created!! foreach subj (HS_001 HS_003 HS_006 HS_007 HS_008 HS_009 HS_011 HS_012 HS_013 SAD_002 SAD_003 SAD_006 SAD_018 SAD_019) ##mapping drawn labels to an individual subject - STARTING AT THE FREESURFER SUBJECTS FOLDER echo {$subj} mri_label2label --srclabel hypothalamus.label --srcsubject HSAverage --trglabel hypothalamus.label --trgsubject {$subj} --regmethod volume mri_label2label --srclabel PAG.label --srcsubject HSAverage --trglabel PAG.label --trgsubject {$subj} --regmethod volume mri_label2label --srclabel SMA.label --srcsubject fsaverage --trglabel SMA.label --trgsubject {$subj} --regmethod volume mri_label2label --srclabel lh.DLPFC.label --srcsubject fsaverage --trglabel lh.DLPFC.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel rh.DLPFC.label --srcsubject fsaverage --trglabel rh.DLPFC.label --trgsubject {$subj} --regmethod surface --hemi rh mri_label2label --srclabel rh.dmPFC.label --srcsubject fsaverage --trglabel rh.dmPFC.label --trgsubject {$subj} --regmethod surface --hemi rh mri_label2label --srclabel lh.dmPFC.label --srcsubject fsaverage --trglabel lh.dmPFC.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel rh.pIns.label --srcsubject fsaverage --trglabel rh.pIns.label --trgsubject {$subj} --regmethod surface --hemi rh mri_label2label --srclabel lh.pIns.label --srcsubject fsaverage --trglabel lh.pIns.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel lh.aIns.label --srcsubject fsaverage --trglabel lh.aIns.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel rh.aIns.label --srcsubject fsaverage --trglabel rh.aIns.label --trgsubject {$subj} --regmethod surface --hemi rh mri_label2label --srclabel rh.mIns.label --srcsubject fsaverage --trglabel rh.mIns.label --trgsubject {$subj} --regmethod surface --hemi rh mri_label2label --srclabel lh.mIns.label --srcsubject fsaverage --trglabel lh.mIns.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel lh.S2.label --srcsubject fsaverage --trglabel lh.S2.label --trgsubject {$subj} --regmethod surface --hemi lh mri_label2label --srclabel rh.S2.label --srcsubject fsaverage --trglabel rh.S2.label --trgsubject {$subj} --regmethod surface --hemi rh cd /export/data2/PI/training/beachpau/Beach_FreeSurfer_data/{$subj}/mri/ mri_label2vol --label ../label/hypothalamus.label --regheader aparc+aseg.mgz --o ROI_FS_hypothalamus.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/PAG.label --regheader aparc+aseg.mgz --o ROI_FS_PAG.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.DLPFC.label --regheader aparc+aseg.mgz --o ROI_FS_rh.DLPFC.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.DLPFC.label --regheader aparc+aseg.mgz --o ROI_FS_lh.DLPFC.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.aIns.label --regheader aparc+aseg.mgz --o ROI_FS_lh.aIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.aIns.label --regheader aparc+aseg.mgz --o ROI_FS_rh.aIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.pIns.label --regheader aparc+aseg.mgz --o ROI_FS_lh.pIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.pIns.label --regheader aparc+aseg.mgz --o ROI_FS_rh.pIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.mIns.label --regheader aparc+aseg.mgz --o ROI_FS_rh.mIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.mIns.label --regheader aparc+aseg.mgz --o ROI_FS_lh.mIns.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.S2.label --regheader aparc+aseg.mgz --o ROI_FS_lh.S2.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.S2.label --regheader aparc+aseg.mgz --o ROI_FS_rh.S2.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/SMA.label --regheader aparc+aseg.mgz --o ROI_FS_SMA.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/rh.dmPFC.label --regheader aparc+aseg.mgz --o ROI_FS_rh.dmPFC.nii.gz --temp orig/001.mgz mri_label2vol --label ../label/lh.dmPFC.label --regheader aparc+aseg.mgz --o ROI_FS_lh.dmPFC.nii.gz --temp orig/001.mgz cd ../ #To deconstruct the aparc.annot files: Done in the subject’s main folder - then copy over labels to subject's 'labels' folder mri_annotation2label --subject {$subj} --hemi rh --outdir ./labels mri_annotation2label --subject {$subj} --hemi lh --outdir ./labels cd $SUBJECTS_DIR cp rh.aparc.annot.avgs.ctab {$subj}/labels cp lh.aparc.annot.avgs.ctab {$subj}/labels cd {$subj}/label cp lh.aIns.label ../labels cp lh.DLPFC.label ../labels cp lh.dmPFC.label ../labels cp lh.mIns.label ../labels cp lh.pIns.label ../labels cp lh.S2.label ../labels cp lh.SMA.label ../labels cp rh.aIns.label ../labels cp rh.DLPFC.label ../labels cp rh.dmPFC.label ../labels cp rh.mIns.label ../labels cp rh.pIns.label ../labels cp rh.S2.label ../labels cp rh.SMA.label ../labels #mris_label2annot command - putting deconstructed annot and new labels together into a new annot file - left hemi then right hemi - new annot files are in subj's 'mri' folder cd /export/data2/PI/training/beachpau/Beach_FreeSurfer_data/{$subj}/labels mris_label2annot --s {$subj} --h lh --ctab lh.aparc.annot.avgs.ctab --annot aug_aparc \ --l lh.bankssts.label \ --l lh.caudalanteriorcingulate.label \ --l lh.caudalmiddlefrontal.label \ --l lh.cuneus.label \ --l lh.entorhinal.label \ --l lh.frontalpole.label \ --l lh.fusiform.label \ --l lh.inferiorparietal.label \ --l lh.inferiortemporal.label \ --l lh.insula.label \ --l lh.isthmuscingulate.label \ --l lh.lateraloccipital.label \ --l lh.lateralorbitofrontal.label \ --l lh.lingual.label \ --l lh.medialorbitofrontal.label \ --l lh.middletemporal.label \ --l lh.paracentral.label \ --l lh.parahippocampal.label \ --l lh.parsopercularis.label \ --l lh.parsorbitalis.label \ --l lh.parstriangularis.label \ --l lh.pericalcarine.label \ --l lh.postcentral.label \ --l lh.posteriorcingulate.label \ --l lh.precentral.label \ --l lh.precuneus.label \ --l lh.rostralanteriorcingulate.label \ --l lh.rostralmiddlefrontal.label \ --l lh.superiorfrontal.label \ --l lh.superiorparietal.label \ --l lh.superiortemporal.label \ --l lh.supramarginal.label \ --l lh.temporalpole.label \ --l lh.transversetemporal.label \ --l lh.aIns.label \ --l lh.mIns.label \ --l lh.pIns.label \ --l lh.S2.label \ --l lh.SMA.label \ --l lh.DLPFC.label \ --l lh.dmPFC.label \ --nhits nhits.mgh mris_label2annot --s {$subj} --h rh --ctab rh.aparc.annot.avgs.ctab --annot aug_aparc \ --l rh.bankssts.label \ --l rh.caudalanteriorcingulate.label \ --l rh.caudalmiddlefrontal.label \ --l rh.cuneus.label \ --l rh.entorhinal.label \ --l rh.frontalpole.label \ --l rh.fusiform.label \ --l rh.inferiorparietal.label \ --l rh.inferiortemporal.label \ --l rh.insula.label \ --l rh.isthmuscingulate.label \ --l rh.lateraloccipital.label \ --l rh.lateralorbitofrontal.label \ --l rh.lingual.label \ --l rh.medialorbitofrontal.label \ --l rh.middletemporal.label \ --l rh.paracentral.label \ --l rh.parahippocampal.label \ --l rh.parsopercularis.label \ --l rh.parsorbitalis.label \ --l rh.parstriangularis.label \ --l rh.pericalcarine.label \ --l rh.postcentral.label \ --l rh.posteriorcingulate.label \ --l rh.precentral.label \ --l rh.precuneus.label \ --l rh.rostralanteriorcingulate.label \ --l rh.rostralmiddlefrontal.label \ --l rh.superiorfrontal.label \ --l rh.superiorparietal.label \ --l rh.superiortemporal.label \ --l rh.supramarginal.label \ --l rh.temporalpole.label \ --l rh.transversetemporal.label \ --l rh.aIns.label \ --l rh.mIns.label \ --l rh.pIns.label \ --l rh.S2.label \ --l rh.SMA.label \ --l rh.DLPFC.label \ --l rh.dmPFC.label \ --nhits nhits.mgh # mri_aparc2aseg step: Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). cd ../ mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon {$subj} mri_aparc2aseg --s {$subj} --annot aug_aparc --noribbon --o aug_aparc+aseg.mgz mv aug_aparc+aseg.mgz mri #For ROIs already in the LUT - and those that have been changed into aug_gmroi volumes cd mri mri_label2vol --seg aug_aparc+aseg.mgz --regheader aug_aparc+aseg.mgz --o aug_gmroi_volume.nii.gz --temp orig/001.mgz mri_label2vol --seg aparc+aseg.mgz --regheader aparc+aseg.mgz --o gmroi_volume.nii.gz --temp orig/001.mgz ##Copy output to subjects' Afni_analy folder cd ../../../AD_Proj/{$subj}/subj/Afni_analy_new/ rm ROI_FS_* rm gmroi_volume.nii.gz rm aug_gmroi_volume.nii.gz cd /export/data2/PI/training/beachpau/Beach_FreeSurfer_data/{$subj}/mri cp ROI_FS_* ../../../AD_Proj/{$subj}/subj/Afni_analy_new/ cp gmroi_volume.nii.gz ../../../AD_Proj/{$subj}/subj/Afni_analy_new/ cp aug_gmroi_volume.nii.gz ../../../AD_Proj/{$subj}/subj/Afni_analy_new/ ##Extract individual ROIs from those already segmented in the LUT cd ../../../AD_Proj/{$subj}/subj/Afni_analy_new/ 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1036)' -prefix ROI_FS_lh.aIns.test.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2036)' -prefix ROI_FS_rh.aIns.test.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1037)' -prefix ROI_FS_lh.mIns.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2037)' -prefix ROI_FS_rh.mIns.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1038)' -prefix ROI_FS_lh.pIns.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2038)' -prefix ROI_FS_rh.pIns.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1042)' -prefix ROI_FS_lh.dmPFC.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2042)' -prefix ROI_FS_rh.dmPFC.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1041)' -prefix ROI_FS_lh.DLPFC.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2041)' -prefix ROI_FS_rh.DLPFC.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1040)' -prefix ROI_FS_lh.SMA.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2040)' -prefix ROI_FS_rh.SMA.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,1039)' -prefix ROI_FS_lh.S2.nii.gz 3dcalc -a aug_gmroi_volume.nii.gz -expr 'equals(a,2039)' -prefix ROI_FS_rh.S2.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1014)' -prefix ROI_FS_lh.vmPFC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,2014)' -prefix ROI_FS_rh.vmPFC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1002)' -prefix ROI_FS_lh.aMCC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,2002)' -prefix ROI_FS_rh.aMCC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1026)' -prefix ROI_FS_lh.rACC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,2026)' -prefix ROI_FS_rh.rACC.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,17)' -prefix ROI_FS_lh.hippocampus.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,53)' -prefix ROI_FS_rh.hippocampus.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,18)' -prefix ROI_FS_lh.amygdala.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,54)' -prefix ROI_FS_rh.amygdala.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,11)' -prefix ROI_FS_lh.caudate.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,50)' -prefix ROI_FS_rh.caudate.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,2011)' -prefix ROI_FS_rh.lateraloccipital.nii.gz 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1011)' -prefix ROI_FS_lh.lateraloccipital.nii.gz ##Must combine a few ROIs in AFNI space and make Thalamic ROIs '.nii.gz' format 3dcalc -a ROI_FS_lh.dmPFC.nii.gz -b ROI_FS_rh.dmPFC.nii.gz -expr '(a+b)' -prefix ROI_FS_dmPFC.nii.gz 3dcalc -a ROI_FS_lh.vmPFC.nii.gz -b ROI_FS_rh.vmPFC.nii.gz -expr '(a+b)' -prefix ROI_FS_vmPFC.nii.gz 3dcalc -a ROI_FS_lh.aMCC.nii.gz -b ROI_FS_rh.aMCC.nii.gz -expr '(a+b)' -prefix ROI_FS_aMCC.nii.gz 3dcalc -a ROI_FS_lh.rACC.nii.gz -b ROI_FS_rh.rACC.nii.gz -expr '(a+b)' -prefix ROI_FS_rACC.nii.gz rm *BRIK.nii* 3dAFNItoNIFTI ROI_mdThal+orig* 3dAFNItoNIFTI ROI_vmpoThal+orig* 3dAFNItoNIFTI ROI_vplThal+orig* gzip *Thal.nii* #now, run the prelim analy scripts...this will do seed to whole brain correlation analysis for each ROI rm run_prelim_analy_bandpassed_zhu.s ln -s ../../../AnalyScripts/new_restingstate/run_prelim_analy_bandpassed_zhu.s . run_prelim_analy_bandpassed_zhu.s ##Run paste_all_1Ds.s (output is All_corr_ROIs_concat_bandpassed_corr.1D) rm paste_all_1D_files.s rm All_corr_ROIs_concat_bandpassed_corr.1D ln -s ../../../AnalyScripts/new_restingstate/paste_all_1D_files.s* . paste_all_1D_files.s ## End of the foreach end ##Go to Group_analy folder and run intra ROI correlation stuff - runs the analysis and pastes the output files into a specific folder in Group_analy cd /export/data2/PI/training/beachpau/AD_Proj/Group_analy run_all_correlation_1D.s run_paste_all_1D_files.s echo "finished"