neuroimagen:centiloid
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Table of Contents
SUVR a Centiloid
Modelo lineal
Segun Rowe et. al. la transformacion de SUVR_FBB a Centiloid sigue la relación,
$ CL = 153.4 \times SUVR_{FBB} - 154.9 $
Esto es sencillo de implementar pero antes hay que calibrar el metodo de obtencion de SUVR de la pipeline con las imagenes procedentes de GAAIN.
Comparando con GAAIN
Basicamente descargamos las imagenes y los valores de centiloid calculados en GAAIN,
https://www.gaaindata.org/data/centiloid/FBBproject_E-25_MR.zip
https://www.gaaindata.org/data/centiloid/FBBproject_E-25_FBB_90110.zip
https://www.gaaindata.org/data/centiloid/FBBproject_SupplementaryTable.xlsx
Y hemos de compara los valores de centiloid obtenidos por nuestra pipeline con los valores obtenidos en GAAIN.
Voy a hacer un proyecto nuevo para esto y voy a copiar alli todos los archivos. Las imagenes vienen DICOM, asi que hay que convertirlas,
[osotolongo@detritus centiloid]$ tree MRDCM/ MRDCM/ ├── 1008_MR │ ├── 100.dcm │ ├── 101.dcm │ ├── 102.dcm │ ├── 103.dcm │ ├── 104.dcm │ ├── 105.dcm │ ├── 106.dcm │ ├── 107.dcm │ ├── 108.dcm │ ├── 109.dcm │ ├── 10.dcm ........ [osotolongo@detritus centiloid]$ tree FBBDCM/ FBBDCM/ ├── 1008_PET_FBB │ ├── 10.dcm │ ├── 11.dcm │ ├── 12.dcm │ ├── 13.dcm │ ├── 14.dcm │ ├── 15.dcm │ ├── 16.dcm │ ├── 17.dcm │ ├── 18.dcm │ ├── 19.dcm │ ├── 1.dcm ..............
Alla vamos. Creo el csv del proyecto,
[osotolongo@detritus centiloid]$ ls MRDCM/ | sed 's/\(.*\)_MR/\1;sub/' > centiloid.csv
A ver como convertimos,
[osotolongo@detritus centiloid]$ dcm2niix -z y -o tmp/ MRDCM/1008_MR/ Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux) Found 176 DICOM file(s) Convert 176 DICOM as tmp/1008_MR_t1_mprage_sag_p2_iso_1.0_20161003101650_2 (256x256x176x1) compress: "/usr/local/mricron/pigz_mricron" -n -f -6 "tmp/1008_MR_t1_mprage_sag_p2_iso_1.0_20161003101650_2.nii" Conversion required 1.217848 seconds (0.450000 for core code). [osotolongo@detritus centiloid]$ ls tmp/ 1008_MR_t1_mprage_sag_p2_iso_1.0_20161003101650_2.json 1008_MR_t1_mprage_sag_p2_iso_1.0_20161003101650_2.nii.gz [osotolongo@detritus centiloid]$ for x in MRDCM/*; do y=$(echo ${x} | sed 's/.*\/\(.*\)_.*/sub\1s0001/'); dcm2niix -z y -o tmp/ ${x}; t=$(ls tmp/*.nii.gz); mv ${t} mri/${y}.nii.gz; mv ${t%.nii.gz}.json mri/${y}.json; done [osotolongo@detritus centiloid]$ ls mri sub1008s0001.json sub1015s0001.json sub1022s0001.json sub1026s0001.json sub1030s0001.json sub1034s0001.json sub1038s0001.json sub2017s0001.json sub2032s0001.json sub1008s0001.nii.gz sub1015s0001.nii.gz sub1022s0001.nii.gz sub1026s0001.nii.gz sub1030s0001.nii.gz sub1034s0001.nii.gz sub1038s0001.nii.gz sub2017s0001.nii.gz sub2032s0001.nii.gz sub1009s0001.json sub1018s0001.json sub1023s0001.json sub1028s0001.json sub1031s0001.json sub1036s0001.json sub2002s0001.json sub2029s0001.json sub1009s0001.nii.gz sub1018s0001.nii.gz sub1023s0001.nii.gz sub1028s0001.nii.gz sub1031s0001.nii.gz sub1036s0001.nii.gz sub2002s0001.nii.gz sub2029s0001.nii.gz sub1010s0001.json sub1019s0001.json sub1024s0001.json sub1029s0001.json sub1032s0001.json sub1037s0001.json sub2005s0001.json sub2030s0001.json sub1010s0001.nii.gz sub1019s0001.nii.gz sub1024s0001.nii.gz sub1029s0001.nii.gz sub1032s0001.nii.gz sub1037s0001.nii.gz sub2005s0001.nii.gz sub2030s0001.nii.gz [osotolongo@detritus centiloid]$ dcm2niix -z y -o tmp/ FBBDCM/1008_PET_FBB/ Chris Rorden's dcm2niiX version v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux) Found 90 DICOM file(s) Convert 90 DICOM as tmp/1008_PET_FBB_Austin_18F_Neuro_Res_20160627143414_43180 (128x128x90x1) compress: "/usr/local/mricron/pigz_mricron" -n -f -6 "tmp/1008_PET_FBB_Austin_18F_Neuro_Res_20160627143414_43180.nii" Conversion required 1.233496 seconds (0.170000 for core code). [osotolongo@detritus centiloid]$ ls tmp 1008_PET_FBB_Austin_18F_Neuro_Res_20160627143414_43180.json 1008_PET_FBB_Austin_18F_Neuro_Res_20160627143414_43180.nii.gz [osotolongo@detritus centiloid]$ for x in FBBDCM/*; do y=$(echo ${x} | sed 's/.*\/\(.*\)_PET_FBB/sub\1s0001/'); dcm2niix -z y -o tmp/ ${x}; t=$(ls tmp/*.nii.gz); mv ${t} fbb/${y}.nii.gz; mv ${t%.nii.gz}.json fbb/${y}.json; done [osotolongo@detritus centiloid]$ ls fbb sub1008s0001.json sub1015s0001.json sub1022s0001.json sub1026s0001.json sub1030s0001.json sub1034s0001.json sub1038s0001.json sub2017s0001.json sub2032s0001.json sub1008s0001.nii.gz sub1015s0001.nii.gz sub1022s0001.nii.gz sub1026s0001.nii.gz sub1030s0001.nii.gz sub1034s0001.nii.gz sub1038s0001.nii.gz sub2017s0001.nii.gz sub2032s0001.nii.gz sub1009s0001.json sub1018s0001.json sub1023s0001.json sub1028s0001.json sub1031s0001.json sub1036s0001.json sub2002s0001.json sub2029s0001.json sub1009s0001.nii.gz sub1018s0001.nii.gz sub1023s0001.nii.gz sub1028s0001.nii.gz sub1031s0001.nii.gz sub1036s0001.nii.gz sub2002s0001.nii.gz sub2029s0001.nii.gz sub1010s0001.json sub1019s0001.json sub1024s0001.json sub1029s0001.json sub1032s0001.json sub1037s0001.json sub2005s0001.json sub2030s0001.json sub1010s0001.nii.gz sub1019s0001.nii.gz sub1024s0001.nii.gz sub1029s0001.nii.gz sub1032s0001.nii.gz sub1037s0001.nii.gz sub2005s0001.nii.gz sub2030s0001.nii.gz
Preparamos y lanzamos FS,
[osotolongo@detritus centiloid]$ fsl2fs.pl centiloid [osotolongo@detritus centiloid]$ precon.pl centiloid Submitted batch job 15673 [osotolongo@detritus centiloid]$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 15673 devel fs_recon osotolon PD 0:00 1 (Dependency) 15648 devel fs_recon osotolon R 0:05 1 brick01 15649 devel fs_recon osotolon R 0:05 1 brick01 15650 devel fs_recon osotolon R 0:05 1 brick01 15651 devel fs_recon osotolon R 0:05 1 brick01 15652 devel fs_recon osotolon R 0:05 1 brick01 15653 devel fs_recon osotolon R 0:05 1 brick01 15654 devel fs_recon osotolon R 0:05 1 brick01 15655 devel fs_recon osotolon R 0:05 1 brick01 15656 devel fs_recon osotolon R 0:05 1 brick01 15657 devel fs_recon osotolon R 0:05 1 brick01 15658 devel fs_recon osotolon R 0:05 1 brick01 15659 devel fs_recon osotolon R 0:05 1 brick01 15660 devel fs_recon osotolon R 0:05 1 brick01 15661 devel fs_recon osotolon R 0:05 1 brick01 15662 devel fs_recon osotolon R 0:05 1 brick01 15663 devel fs_recon osotolon R 0:05 1 brick01 15664 devel fs_recon osotolon R 0:02 1 brick01 15665 devel fs_recon osotolon R 0:02 1 brick01 15666 devel fs_recon osotolon R 0:02 1 brick01 15667 devel fs_recon osotolon R 0:02 1 brick01 15668 devel fs_recon osotolon R 0:02 1 brick01 15669 devel fs_recon osotolon R 0:02 1 brick01 15670 devel fs_recon osotolon R 0:02 1 brick01 15671 devel fs_recon osotolon R 0:02 1 brick01 15672 devel fs_recon osotolon R 0:02 1 brick01
neuroimagen/centiloid.1554803328.txt.gz · Last modified: 2020/08/04 10:45 (external edit)
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