====== 3dmaskave_grp ======
''3dmaskave_grp'' [[https://github.com/LabNeuroCogDevel/lncdtools/blob/master/3dmaskave_grp|(source on github)]] is an abstracted version of  ''07_extract*.bash'' that saves a csv with columns like ''roimask,subjid,inputname,mean_val'' 

It is in the default path on [[:admin:it:rhea]]. See ''3dmaskave_grp -help'' for complete reference.


The command takes any number of ''-mask'' arguments. Masks can just be a mask file (and the name column in the output will be a safe basename of that) or you can label the mask by prefacing with e.g. ''myroiname=a''.


A call like

<code=bash>
3dmaskave_grp -csv MPFC-ACC_1.csv \
 -mask 'ACC=mvm/ACC_p2-16_cl40.nii.gz<1>' \
 -mask 'ROI2=mvm/ACC_p2-16_cl40.nii.gz<2>' \
 -mask 'mvm/ACC_p2-16_cl40.nii.gz<3>' \
 -- /Volumes/Hera/Projects/7TBrainMech/subjs/101*/conn_mrsi_rest/mxcovsph/08-MPFC_deconreml-r.nii.gz
</code>
yields

<code>
grep -h 1012 MPFC-ACC_1.csv 
 ACC,10129_20180917,08-MPFC_deconreml-r,0.219054
 ROI2,10129_20180917,08-MPFC_deconreml-r,0.040569
 ACC_p2_16_cl40_3,10129_20180917,08-MPFC_deconreml-r,-0.162038
</code>


You may also use an [[:tools:AFNI]] style [[:tools:3dMVM]]/3dLME datatable to specify and label inputs.
<code>
3dmaskave_grp -datatable datatable.tsv -label_col 2,3 -csv myout.csv
</code>