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neuroimagen:fs_group_analysis [2020/07/17 08:14]
osotolongo [bulk processing]
neuroimagen:fs_group_analysis [2020/08/04 10:58] (current)
Line 368: Line 368:
     32  COMPOSITE_languge_naming      32  COMPOSITE_languge_naming 
     33  EstimatedTotalIntraCranialVol     33  EstimatedTotalIntraCranialVol
 +</code>
 +
 +Ahora ir escogiendo y pegando,
 +
 +<code bash>
 +osotolongo@detritus:facehbi$ awk -F"," {'print $3","$6","$7","$8","$9","$33'} datacomb_freesurfer_neuro_v0_scdSUMCC_icv.csv | sed 's/.*\/facehbi_/facehbi_/;s/SubjID/Variables/;s/edat/age/;s/Anyos_Escolaridad_FAC/education/;s/Sex_1H_0M/gender/;s/facehbi_\([^,]*\),/Input facehbi_\1 Main /; s/,/ /g' > scd9a.tsv
 +osotolongo@detritus:facehbi$ head scd9a.tsv
 +Variables age education gender SCDplus_Memorycomplaint EstimatedTotalIntraCranialVol
 +Input facehbi_0001 Main 71 8 0 0 1756453.4998
 +Input facehbi_0002 Main 70 12 1 0 1529412.17649
 +Input facehbi_0003 Main 70 8 0 0 1326413.64353
 +Input facehbi_0004 Main 76 16 0 0 1368330.41095
 +Input facehbi_0005 Main 68 20 1 0 1467058.62476
 +Input facehbi_0006 Main 64 14 0 0 1300087.33412
 +Input facehbi_0007 Main 59 19 1 1 1672996.58646
 +Input facehbi_0008 Main 55 16 0 0 1230515.65242
 +Input facehbi_0009 Main 67 16 0 0 1526642.95225
 +osotolongo@detritus:facehbi$ cat scd9a.header 
 +GroupDescriptorFile 1
 +Title FACEHBI_SCDplus_Memorycomplaint
 +Class Main
 +osotolongo@detritus:facehbi$ cat scd9a.header scd9a.tsv > scd9a.fsgd
 +osotolongo@detritus:facehbi$ head scd9a.fsgd
 +GroupDescriptorFile 1
 +Title FACEHBI_SCDplus_Memorycomplaint
 +Class Main
 +Variables age education gender SCDplus_Memorycomplaint EstimatedTotalIntraCranialVol
 +Input facehbi_0001 Main 71 8 0 0 1756453.4998
 +Input facehbi_0002 Main 70 12 1 0 1529412.17649
 +Input facehbi_0003 Main 70 8 0 0 1326413.64353
 +Input facehbi_0004 Main 76 16 0 0 1368330.41095
 +Input facehbi_0005 Main 68 20 1 0 1467058.62476
 +Input facehbi_0006 Main 64 14 0 0 1300087.33412
 +
 +osotolongo@detritus:facehbi$ cat compsa.mtx 
 +0 0 0 0 1 0
 +
 +</code>
 +
 +El codigo debe cambiar algo, 
 +
 +<code bash fsgda.sh>
 +avar=$1
 +shift
 +mris_preproc --fsgd ${avar}.fsgd --cache-in area.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.${avar}.area.10.mgh
 +mris_preproc --fsgd ${avar}.fsgd --cache-in area.fwhm10.fsaverage --target fsaverage --hemi rh --out rh.${avar}.area.10.mgh
 +mri_glmfit --y lh.${avar}.area.10.mgh --fsgd ${avar}.fsgd --C compsa.mtx --surf fsaverage lh --cortex --glmdir lh.${avar}.sa.glmdir
 +mri_glmfit --y rh.${avar}.area.10.mgh --fsgd ${avar}.fsgd --C compsa.mtx --surf fsaverage rh --cortex --glmdir rh.${avar}.sa.glmdir
 +mri_glmfit-sim --glmdir lh.${avar}.sa.glmdir --cache 4 neg --cwp 0.05 --2spaces
 +mri_glmfit-sim --glmdir rh.${avar}.sa.glmdir --cache 4 neg --cwp 0.05 --2spaces
 +mri_glmfit-sim --glmdir lh.${avar}.sa.glmdir --cache 4 pos --cwp 0.05 --2spaces
 +mri_glmfit-sim --glmdir rh.${avar}.sa.glmdir --cache 4 pos --cwp 0.05 --2spaces
 +echo "lh, neg"
 +grep -v "#" lh.${avar}.sa.glmdir/compsa/cache.th40.neg.sig.cluster.summary
 +echo "rh, neg"
 +grep -v "#" rh.${avar}.sa.glmdir/compsa/cache.th40.neg.sig.cluster.summary
 +echo "lh, pos"
 +grep -v "#" lh.${avar}.sa.glmdir/compsa/cache.th40.pos.sig.cluster.summary
 +echo "rh, pos"
 +grep -v "#" rh.${avar}.sa.glmdir/compsa/cache.th40.pos.sig.cluster.summary
 +</code>
 +
 +No hay demasiados resultados pero alguno si,
 +
 +<code bash>
 +osotolongo@detritus:facehbi$ ./fsgda.sh scd16a
 +...
 +...
 +...
 +lh, neg
 +rh, neg
 +lh, pos
 +          4.160   87102    125.74    -25.2  -79.5   13.8  0.03135  0.02820  0.03450    252      991.50  superiorparietal
 +rh, pos
 +</code>
 +
 +ahi ya sabemos donde buscar,
 +
 +<code bash>
 +osotolongo@detritus:facehbi$ cat scd16a.header 
 +GroupDescriptorFile 1
 +Title FACEHBI_SCDplus_SUVRgt1.35
 +Class Main
 +
 +osotolongo@detritus:facehbi$ cat lh.scd16a.sa.glmdir/compsa/cache.th40.pos.sig.cluster.summary
 +...
 +...
 +...
 +# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs    WghtVtx   Annot
 +          4.160   87102    125.74    -25.2  -79.5   13.8  0.03135  0.02820  0.03450    252      991.50  superiorparietal
 +</code>
 +
 +
 +Otros resultados, 
 +
 +<code>
 +scd17a
 +
 +lh, neg
 +rh, neg
 +lh, pos
 +          5.013  112180    428.88    -32.5  -81.3   14.8  0.00020  0.00000  0.00040    714     3121.90  inferiorparietal
 +rh, pos
 +
 +
 </code> </code>
  
  
neuroimagen/fs_group_analysis.1594973645.txt.gz ยท Last modified: 2020/08/04 10:47 (external edit)