How to use inpolygon or other tool to mask netcdf with different lat/lon matrix size to shapefile having different lat/lon matrix size?

I am trying to mask netcdf (unable to attach as zip file exceeds 5MB) based on a Mississippi river basin shapefile(attached) using inpolygon. But I get this following error:

Arrays have incompatible sizes for this operation.

Error in inpolygon (line 76)

mask = (x >= min(xv)) & (x <= max(xv)) & (y>=min(yv)) & (y<=max(yv));

Error in plot_soilice (line 10)

[in,on] = inpolygon(lon,lat,C.X,C.Y);

Below is the code I used:

%% shape must be in lat Lon projection
C = shaperead('\MRB_Shapefile\mrb.shp');
%shapeinfo('\Miss_RiverBasin\Miss_RiverBasin.shp');
%corresponding name of lat, Lon and variable at netcdf
% lat and lon are matrixes of, like.. lat[nrow,ncol] .. same for var[nrow,ncol]
lat=ncread('\Noah.monthlymean.01.nc','lat');
lon=ncread('\Noah.monthlymean.01.nc','lon');
SMC=ncread('\\Noah.monthlymean.01.nc','SMC');
SMC_n = squeeze(SMC(:,1,:));
[in,on] = inpolygon(lon,lat,C.X,C.Y);
numel(lat(~in)) + numel(lat(in)); % must be the same size of ncol*nrow in var[nrow,ncol]
%in2 is the mask used to extract the values
in2 = double(in);
clf
mymap=pcolor(lon,lat,in2); %plot mask to verify, Is it what you want?
%%based on the indexes you can calculate max, min, mean.... whatever you want... 

I assume this will happen with any shapefile as the lat lon grids of shapefile will be different from the netcdf lat/lon grids. Eventually, the matrices of lat/lon from shapefile and netcdf lat/lon matrice will always be different. So, I am looking for a generic solution that can be applied for any shapefile and any netcdf file meaning different matrix sizes of lat lon. Does anybody have any suggestions for this problem and a generic solution?

Any suggestions or help is appreciated.

Thanks

[J A]

Matlab Community,

Please suggest or let me know if something is unclear in the question.

I appreciate your time and effort.

Thanks