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Makefile
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step2:
python3 procADNICluster.py --cluster --timeLimit 40 --step 2 --printOnly --freesurfVS 6
step4:
python3 procADNICluster.py --cluster --timeLimit 20 --step 4
lh_m5:
echo "/share/apps/python-3.5.1/bin/python3 /home/rmarines/phd/mres/voxelwiseDPM/launchADNIthick.py --dataset Lh --firstModel 5 --lastModel 5 --nrOuterIter 30 --nrInnerIter 2 --nrClust 4"| qsub -S /bin/bash -l tmem=31.7G -l h_vmem=31.7G -l h_rt=10:15:0 -N Lh_m5 -j y -wd /home/rmarines/phd_proj/voxelwiseDPM/clusterOutputADNI
blend_col:
file=resfiles/adniThMo10kCl4_VWDPMLinear/params_o30.npz blender --background --python blenderCol.py
atrophyMapFVPCA:
freeview -f /usr/local/freesurfer-5.3.0/subjects/fsaverage/surf/lh.inflated:overlay=resfiles/drc10kavgThickMapFWHM0PCA:overlay_threshold=-1.3,-0.46 --viewport 3d
# canonical correlation between cog tests and vertex-wise cortical thickness measures
cca:
python3 drcThickCCA.py --dataset avg --fwhmLevel 0
# run vertex clustering model (standard one) dataset: ADNI avg - assumes uninformative prior on subject-shift params
adniThickAvgFWHM0Cl3K-meansRa1Pr0_VWDPMMean:
python3 launchThick.py --launcherScript adniThick.py --dataset avg --fwhmLevel 0 --firstInstance 0 --lastInstance 0 --nrProc 10 --models 8 --nrOuterIt 15 --nrInnerIt 1 --nrClust 3 --initClustering k-means --rangeFactor 1 --serial
# run vertex clustering model (the ROI average version) dataset: DRC avg - assumes uninformative prior on subject-shift params
drcThickAvgFWHM0Cl3HistRa1Pr0_VDPMMean:
python3 launchThick.py --launcherScript drcThick.py --dataset avg --fwhmLevel 0 --firstInstance 1 --lastInstance 1 --nrProc 1 --models 4 --nrOuterIt 25 --nrInnerIt 1 --nrClust 3 --initClustering hist --rangeFactor 1 --serial
clearJobs:
qstat | awk '{ if ($$5 == "Eqw") print $$1;}' | xargs qmod -cj
deleteAllJobs:
qstat | awk '{print $1;}' | xargs qdel
printJobsNotDoneADNI:
python3 printJobsNotDone.py --clustOutputFolder clusterOutputADNI
printGtmsegNotDoneADNI:
python3 printJobsNotDone.py --clustOutputFolder clusterOutputADNI --doneStr "gtmseg Done"
colorAdniThickMRF:
file=resfiles/adniThavgFWHM0Initk-meansCl3Pr0Ra1Mrf5_VDPM_MRF/clust0_adniThavgFWHM0Initk-meansCl3Pr0Ra1Mrf5_VDPM_MRF.npz pngFile=resfiles/adniThavgFWHM0Initk-meansCl3Pr0Ra1Mrf5_VDPM_MRF/clust0_adniThavgFWHM0Initk-meansCl3Pr0Ra1Mrf5_VDPM_MRF.png blender --background --python colorClustProb.py
adniThickClustList:
python3 launchThick.py --launcherScript adniThick.py --firstInstance 1 --lastInstance 1 --nrProc 1 --models 9 --nrOuterIt 15 --nrInnerIt 1 --nrClustList 2,3,4,5,6,7,8,9,10,12,15,20,30,40,50,60,70,80,90,100 --initClustering k-means --rangeFactor 0 --informPrior 1 --cluster --timeLimit 23
qstatFullJobName:
qstat -xml | tr '\n' ' ' | sed 's#<job_list[^>]*>#\n#g' | sed 's#<[^>]*>##g' | grep " " | column -t
copyThickness:
rsync -av --include="*h.thickness.fwhm*" --include="*/" --exclude="*" "rmarines@comic100:/home/rmarines/VWDPM/ADNI_data/MP-Rage_proc_all/subjects/" .
adniPetManyClust:
python3 launchThick.py --launcherScript adniPet.py --firstInstance 1 --lastInstance 1 --nrProc 1 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClustList 18,19,20,21,22,23,24,25,26,27,28,29,30,32,34,36,38,40,42,44,46,48,50 --initClustering k-means --rangeFactor 1 --informPrior 0 --cluster --timeLimit 23
copyToPublicRepo:
cp -r adniCommon.py adniPet.py adniThick.py aux.py blenderCol.py colorAtrophyExtent.py colorClustProb.py colorClustSlope.py colorDiffs.py colorVerticesDirectly.py env.py launchCommon.py launchSynth.py launchThick.py plotFunc.py PlotterVDPM.py procADNICluster.py procADNIMerge.py procADNIPET.py procPETMerge.py synthCommon.py synthMRF.py synth.py tadpole.py VDPMLinear.py VDPMMean.py VDPM_MRF.py VDPMNanMasks.py VDPMNanNonMean.py VDPMNan.py VDPMSimplified.py voxCommon.py voxelDPM.py Makefile ../../research_public/dive/
copySlopeCol:
find . -name "*slopeCol*" | xargs -I {} find {} -name "*.png" | awk '{ split($1,a,"/"); system("cp "$1" "a[2]"/slopeCol.png") }'
# actually not working properly
cmpAnnotAfterRegist:
cd ~/HCP/Downloads/100206/T1w/100206/label; freeview $SUBJECTS_DIR/100206/mri/T1.mgz 100206_labeledVol.nii.gz -f $SUBJECTS_DIR/100206/surf/lh.white $SUBJECTS_DIR/100206/surf/lh.pial:annot=aligned100206.annot; freeview ../mri/T1.mgz labeledVol.nii.gz -f ../surf/lh.white ../surf/lh.pial:annot=lh.100206.aparc.annot
makeHCPFreeSurfLinks:
cd /usr/local/freesurfer-6.0.0/subjects; ls -d /media/razvan/Seagate\ Expansion\ Drive/HCP/Downloads/1*// | awk '{split($3,a,"/"); print(a[4])}' | xargs -I {} sudo ln -s /media/razvan/Seagate\ Expansion\ Drive/HCP/Downloads/{}/T1w/{} {}
####### Main experiments for the paper ########
adniMain:
python3 adniThick.py --fwhmLevel 0 --runIndex 1 --nrProc 1 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 8 --initClustering k-means --rangeFactor 1 --informPrior 0;
drcAdMain:
python3 drcThick.py --fwhmLevel 0 --runIndex 1 --nrProc 1 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 4 --initClustering k-means --rangeFactor 1 --informPrior 0;
drcPcaMain:
python3 drcThick.py --fwhmLevel 0 --runIndex 1 --nrProc 1 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 3 --initClustering k-means --rangeFactor 1 --informPrior 0;
petMain:
python3 adniPet.py --fwhmLevel 0 --runIndex 1 --nrProc 1 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 20 --initClustering k-means --rangeFactor 1 --informPrior 0;
adniMaster:
python3 adniThick.py --fwhmLevel 0 --runIndex 0 --nrProc 10 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 8 --initClustering k-means --rangeFactor 1 --informPrior 0;
petMaster:
python3 adniPet.py --fwhmLevel 0 --runIndex 0 --nrProc 10 --models 9 --nrOuterIt 25 --nrInnerIt 1 --nrClust 20 --initClustering k-means --rangeFactor 1 --informPrior 0;
fourMainExp:
make adniMain;
make drcAdMain;
make drcPcaMain;
make petMain;
# fit model for different centers for each trajectory
synthDifferentTrajCenters:
python3 launchSynth.py --launcherScript synth.py --firstInstance 1 --lastInstance 1 --nrProc 1 --models 8 --expToRun 1 --steps 0 --nrOuterIt 10 --nrInnerIt 1 --nrClustList 3 --initClustering k-means --rangeFactor 0 --informPrior 1
# fit model for different numbers of clusters
synthDifferentNrClust:
python3 launchSynth.py --launcherScript synth.py --firstInstance 1 --lastInstance 1 --nrProc 1 --models 8 --expToRun 2 --steps 0 --nrOuterIt 10 --nrInnerIt 1 --nrClustList 3 --initClustering k-means --rangeFactor 0 --informPrior 1
# fit model for different numbers of subjects
synthDifferentNrSubj:
python3 launchSynth.py --launcherScript synth.py --firstInstance 1 --lastInstance 1 --nrProc 1 --models 8 --expToRun 3 --steps 0 --nrOuterIt 10 --nrInnerIt 1 --nrClustList 3 --initClustering k-means --rangeFactor 0 --informPrior 1
synthAll:
make synthDifferentTrajCenters;
make synthDifferentNrClust;
make synthDifferentNrSubj;
####### 10-fold Cross-Validation experiments on cluster ########
adniThickValidClust:
echo -n '6,9,10' | xargs -I {} -d, /share/apps/python-3.5.1/bin/python3 launchThick.py --launcherScript adniThick.py --firstInstance 1 --lastInstance 10 --nrProc 10 --models {} --nrOuterIt 25 --nrInnerIt 1 --nrClust 8 --initClustering k-means --rangeFactor 1 --informPrior 0 --cluster --timeLimit 23 --mem 31
adniPetValidClust:
echo -n '6,9,10' | xargs -I {} -d, /share/apps/python-3.5.1/bin/python3 launchThick.py --launcherScript adniPet.py --firstInstance 1 --lastInstance 10 --nrProc 10 --models {} --nrOuterIt 25 --nrInnerIt 1 --nrClust 20 --initClustering k-means --rangeFactor 1 --informPrior 0 --cluster --timeLimit 23 --mem 31
###### HCP connectome analysis ########
createHCPpatches:
python3 createHCPpatches.py --runPart 10 --maxSearchRadius 5
copyFromCmicPC:
scp -r 'razvan@128.16.15.167:/home/razvan/phd_proj/voxelwiseDPM/resfiles/*NearNeigh.npz' resfiles;
echo -n 'adniPetInitk-meansCl20Pr0Ra1Mrf5DataNZ_VDPM_MRF,drcThFWHM0Initk-meansCl4Pr0Ra1Mrf5_VDPM_MRFPCA,drcThFWHM0Initk-meansCl3Pr0Ra1Mrf5_VDPM_MRFAD,adniThFWHM0Initk-meansCl8Pr0Ra1Mrf5_VDPM_MRF' | xargs -I {} -d, scp -r 'razvan@128.16.15.167:/home/razvan/phd_proj/voxelwiseDPM/resfiles/{}/*' {};
##### TADPOLE ########
tadpoleLdb:
python3 tadpole.py --runIndex 1 --nrProc 1 --models 13 --nrOuterIt 5 --nrInnerIt 1 --nrClust 12 --initClustering hist --rangeFactor 1 --informPrior 0 --leaderboard 1
tadpoleD2:
python3 tadpole.py --runIndex 1 --nrProc 1 --models 13 --nrOuterIt 5 --nrInnerIt 1 --nrClust 12 --initClustering hist --rangeFactor 1 --informPrior 0 --leaderboard 0
tadpoleD3:
python3 tadpoleD3.py --runIndex 1 --nrProc 1 --models 13 --nrOuterIt 5 --nrInnerIt 1 --nrClust 13 --initClustering hist --rangeFactor 1 --informPrior 0 --leaderboard 0