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Dear All, I think I found the source of the discrepancy. Currently I am using FSL v3.3. avwstats -v (no ++) returns a *slightly* different volume value than avwstats++ fslstats (v4.0.1) returns the same volume value as avwstats++ When I use avwstats (no ++), i get nearly identical numbers as to what is in the *.sienax file: % avwstats 20071129_13_1_stdmaskbrain_pve_0 -m -v 0.050212 7864320 6308232.703233 % avwstats 20071129_13_1_stdmaskbrain_pve_1 -m -v 0.081955 7864320 6308232.703233 % avwstats 20071129_13_1_stdmaskbrain_pve_2 -m -v 0.060953 7864320 6308232.703233 >> csf = 0.050212 * 6308232.703233; >> grey = 0.081955 * 6308232.703233; >> white = 0.060953 * 6308232.703233; >> bpf = ( grey + white ) / ( grey + white + csf ); >> fprintf( 'csf = %.1f grey = %.1f white = %.1f bpf=%.6f \n', csf, grey, white, bpf ); csf = 316749.0 grey = 516991.2 white = 384505.7 bpf=0.739996 From *.sienax file: Class: CSF tissue 1 tissue 2 brain percentage Volumes: 316748.7 516990.9 384503.5 0.739996 Results from avwstats++ are below, but bottom line: csf = 316824.7 grey = 516909.2 white = 384486.8 bpf = 0.7399 I believe that the results generated from sienax/FSL v3.3 would be slightly different from sienax/FSL v4.0.1 due to the use of avwstats v fslstats, respectively. Is this something you see, too? Thanks, - BettyAnn On Wed, 2 Jan 2008 20:11:23 +0000, Bettyann Chodkowski <[log in to unmask]> wrote: >Mark, > >Ah, thanks. This helps a great deal. > >The values I calculate for the tissue classifications are still not exactly the same as what I see >reported in the *.sienax file. The final brain percentage value does match, however. Might you >see something I am doing wrong? i used fsl v3.3 when running sienax but fsl v4.0.1 for fslstats >(which gives the same values as avwstats++ v3.3). > >% fslstats 20071129_13_1_stdmaskbrain_pve_0 -m -v >0.050224 7864320 6308232.500000 >% fslstats 20071129_13_1_stdmaskbrain_pve_1 -m -v >0.081942 7864320 6308232.500000 >% fslstats 20071129_13_1_stdmaskbrain_pve_2 -m -v >0.060950 7864320 6308232.500000 > >in matlab: >>> csf = 0.050224 * 6308232.500000; >>> grey = 0.081942 * 6308232.500000; >>> white = 0.060950 * 6308232.500000; >>> bpf = ( grey + white ) / ( grey + white + csf ) >bpf = 0.7399 >>> fprintf( 'csf = %.1f grey = %.1f white = %.1f \n', csf, grey, white ); >csf = 316824.7 grey = 516909.2 white = 384486.8 > >The tissue volumes in my *.sienax file are: > >Class: CSF tissue 1 tissue 2 brain percentage >Volumes: 316748.7 516990.9 384503.5 0.739996 > >Also, in the snippet of code from the sienax script where the volumes are computed, are you >dividing the result by 1 in the dc calculator? if so, why? > >Thank you for your help, >- BettyAnn >=========================================================== =============