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--- neuroimagen:fs_group_analysis [2020/07/16 09:39] – [Full data] osotolongo
+++ neuroimagen:fs_group_analysis [2020/08/04 10:58] (current) – external edit 127.0.0.1
@@ Line 268: / Line 268: @@
 osotolongo@detritus:facehbi$ grep -v "#" lh.executive_fluency.glmdir/comps/cache.th40.neg.sig.cluster.summary
 osotolongo@detritus:facehbi$ mri_glmfit-sim --glmdir lh.executive_fluency.glmdir --cache 4 pos --cwp 0.05 --2spaces
+osotolongo@detritus:facehbi$ grep -v "#" lh.executive_fluency.glmdir/comps/cache.th40.pos.sig.cluster.summary
+</code>
+Y esto lo hacemos para el otro hemisferio igualmente. Aqui no hay nada asi que podemos seguir hacia la siguiente variable, ;-)
+**ejemplo de resultados**
+<code bash>
+osotolongo@detritus:facehbi$ grep -v "#" lh.executive_processing.glmdir/comps/cache.th40.neg.sig.cluster.summary
+       -6.662  147537    122.63    -24.1  -78.1   17.4  0.00739  0.00579  0.00898    237    -1176.13  superiorparietal
+</code>
+{{ :neuroimagen:sig.png|}}
+{{ :neuroimagen:clusters.png|}}
+===== bulk processing =====
+Esto es muy aburrido, asi que vamos a hacerlo todo junto,
+<code bash fsgd.sh>
+avar=$1
+shift
+mris_preproc --fsgd ${avar}.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.${avar}.thickness.10.mgh
+mris_preproc --fsgd ${avar}.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out rh.${avar}.thickness.10.mgh
+mri_glmfit --y lh.${avar}.thickness.10.mgh --fsgd ${avar}.fsgd --C comps.mtx --surf fsaverage lh --cortex --glmdir lh.${avar}.glmdir
+mri_glmfit --y rh.${avar}.thickness.10.mgh --fsgd ${avar}.fsgd --C comps.mtx --surf fsaverage rh --cortex --glmdir rh.${avar}.glmdir
+mri_glmfit-sim --glmdir lh.${avar}.glmdir --cache 4 neg --cwp 0.05 --2spaces
+mri_glmfit-sim --glmdir rh.${avar}.glmdir --cache 4 neg --cwp 0.05 --2spaces
+mri_glmfit-sim --glmdir lh.${avar}.glmdir --cache 4 pos --cwp 0.05 --2spaces
+mri_glmfit-sim --glmdir rh.${avar}.glmdir --cache 4 pos --cwp 0.05 --2spaces
+echo "lh, neg"
+grep -v "#" lh.${avar}.glmdir/comps/cache.th40.neg.sig.cluster.summary
+echo "rh, neg"
+grep -v "#" rh.${avar}.glmdir/comps/cache.th40.neg.sig.cluster.summary
+echo "lh, pos"
+grep -v "#" lh.${avar}.glmdir/comps/cache.th40.pos.sig.cluster.summary
+echo "rh, pos"
+grep -v "#" rh.${avar}.glmdir/comps/cache.th40.pos.sig.cluster.summary
+</code>
+todavia hay que hacer el archivo fsgd a mano pero despues de eso,
+<code bash>
+osotolongo@detritus:facehbi$ head wms.fsgd
+GroupDescriptorFile 1
+Title FACEHBI_memory_wms
+Class Main
+Variables age education gender memory_WMS
+Input facehbi_0001 Main 71 8 0 -0.453361
+Input facehbi_0002 Main 70 12 1 0.259093
+Input facehbi_0003 Main 70 8 0 -0.809587
+Input facehbi_0004 Main 76 16 0 -0.152722
+Input facehbi_0005 Main 68 20 1 0.630976
+Input facehbi_0006 Main 64 14 0 0.116602
+osotolongo@detritus:facehbi$ ./fsgd.sh wms
+</code>
+===== Surface Area =====
+Tengo que añadir el ICV a los datos, (un poco de awk, sed, join, etc) y deberia quedar,
+<code bash>
+osotolongo@detritus:facehbi$ head -n 1 datacomb_freesurfer_neuro_v0_scdSUMCC_icv.csv | sed 's/,/\n/g' | cat -n
+  code_facehbi
+  Subject
+  SubjID
+  N_Interno
+  Date
+  edat
+  Anyos_Escolaridad_FAC
+  Sex_1H_0M
+  SCDplus_Memorycomplaint
+  SCDplus_APOE4
+  SCDplus_concernsaboutcognition
+  SCDplus_feelingworsethancontemporarypeers
+  SCDplus_informantcorroboratessymptoms
+  SCDplus_onset60Y
+  SCDplus_onsetwithinlast5Y
+  SCDplus_SUVRgt1.35
+  SCDplus_SUVRgt1.45
+  SCDplus_Total7
+  Q_QSM_JPO
+  SUVR
+  Centilod
+  APOE
+  COMPOSITE_executive_fluency
+  COMPOSITE_executive_processing speed
+  COMPOSITE_executive_attention
+  COMPOSITE_memory_FNAME professions
+  COMPOSITE_memory_FNAME names
+  COMPOSITES_memory_WMS
+  COMPOSITE_memory_RBANS
+  COMPOSITE_gnosis
+  COMPOSITE_praxis
+  COMPOSITE_languge_naming
+  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 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>
-Aqui no hay nada asi que podemos seguir hacia la siguiente variable, ;-)