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neuroimagen:fs_group_analysis [2020/07/16 09:56]
osotolongo [Full data]
neuroimagen:fs_group_analysis [2020/07/17 09:12]
osotolongo [Surface Area]
Line 285: Line 285:
  
 {{ :neuroimagen:clusters.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
 +    10  SCDplus_APOE4
 +    11  SCDplus_concernsaboutcognition
 +    12  SCDplus_feelingworsethancontemporarypeers
 +    13  SCDplus_informantcorroboratessymptoms
 +    14  SCDplus_onset60Y
 +    15  SCDplus_onsetwithinlast5Y
 +    16  SCDplus_SUVRgt1.35
 +    17  SCDplus_SUVRgt1.45
 +    18  SCDplus_Total7
 +    19  Q_QSM_JPO
 +    20  SUVR
 +    21  Centilod
 +    22  APOE
 +    23  COMPOSITE_executive_fluency 
 +    24  COMPOSITE_executive_processing speed 
 +    25  COMPOSITE_executive_attention 
 +    26  COMPOSITE_memory_FNAME professions
 +    27  COMPOSITE_memory_FNAME names 
 +    28  COMPOSITES_memory_WMS 
 +    29  COMPOSITE_memory_RBANS 
 +    30  COMPOSITE_gnosis
 +    31  COMPOSITE_praxis
 +    32  COMPOSITE_languge_naming 
 +    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>
 +
 +
 +
  
  
neuroimagen/fs_group_analysis.txt · Last modified: 2020/08/04 10:58 (external edit)