Hello FreeSurfer experts,

I'm planning to run QDEC on Schizophrenia and controls. To do that I ran recon-all for few subjects in 2 different systems. Both systems have ubuntu 16.04 OS but different freesurfer versions. One is using FS version6 and other is FS version5.3.

Just for confirmation, I ran recon-all for the same subjects in 2 above said systems. Now both yield different values for the area. Here I have tabulated the values:

fsid	Left-Lateral-Ventricle	Left-Inf-Lat-Vent	Left-Cerebellum-White-Matter	Left-Cerebellum-Cortex	Left-Thalamus-Proper	Left-Caudate	Left-Putamen	Left-Pallidum	3rd-Ventricle	4th-Ventricle	Brain-Stem	Left-Hippocampus	Left-Amygdala	CSF	Left-Accumbens-area	Left-VentralDC	Left-choroid-plexus	Right-Lateral-Ventricle	Right-Inf-Lat-Vent	Right-Cerebellum-White-Matter	Right-Cerebellum-Cortex	Right-Thalamus-Proper	Right-Caudate	Right-Putamen	Right-Pallidum	Right-Hippocampus	Right-Amygdala	Right-Accumbens-area	Right-VentralDC	Right-choroid-plexus	WM-hypointensities	Optic-Chiasm	CC_Posterior	CC_Mid_Posterior	CC_Central	CC_Mid_Anterior	CC_Anterior
INSP015	16157.6	1227.3	11526.1	50572.8	6893	3228.3	5076.3	1927.7	2698.1	2577.8	17706.7	3525.3	1594.6	1164.3	538	4063.9	889.6	10616.9	1179.4	10638.1	50615.7	7252.9	3612.1	5719.7	1788.7	3852.7	1980.1	504.5	3762.4	748.8	728.9	194.4	854.8	393.8	393.9	425.8	1042.1
INSP015	16157.6	1227.3	11526.1	50572.8	6893	3228.3	5076.3	1927.7	2698.1	2577.8	17706.7	3525.3	1594.6	1164.3	538	4063.9	889.6	10616.9	1179.4	10638.1	50615.7	7252.9	3612.1	5719.7	1788.7	3852.7	1980.1	504.5	3762.4	748.8	728.9	194.4	854.8	393.8	393.9	425.8	1042.1

INSP019	7059.6	296	10820.8	42288.3	6177.2	2785.3	4573.8	1793.4	1283.5	1819.9	18958.5	3546.9	1535.8	1212.9	471.2	3741.7	583.6	7378.3	249.5	10200.6	42803.5	6173.9	3078.5	4617.6	1861.3	3638	1599.3	473.7	3532.6	627.1	591.4	270.3	897.7	443.6	497.5	460.7	798.9
INSP019	6962.9	288.8	11995	44004.4	6471.6	2883.8	4653	1888.6	1285.7	1706.1	18983.8	3619.9	1515.5	1117	493.8	3790.8	620.7	7446.8	273.6	10674.7	42678.1	6220.8	3109.2	4498.1	1943	3540.7	1658.3	499.8	3656.3	652	735.6	189.4	863.6	470.6	434.4	502.6	749.1


IYBA009	10661.7	644	16029.1	61364.8	7534.2	4416.4	5562.8	2279.9	1335.2	1775.6	24381.2	3787.8	1666.3	970.4	624.4	4286.9	709.1	9079.2	803.7	15172.2	59565.1	6989.7	4334.1	5550.7	2267.8	3928.2	1743.1	582.4	4465.2	676.6	728	195.6	667.6	426.8	363.9	362.4	929.1
IYBA009	10730.6	722.5	16662.8	60503.6	7686.1	4328.3	5430.1	2256.9	1365	1720.2	24139.9	3749.1	1635.9	995.6	639.8	4374	573.9	8963.9	795.2	15817.6	60176.1	7044.7	4251.9	5423.8	2241.1	3715.8	1749.2	600.2	4418.1	623.8	953.8	155	664.6	444.3	401.5	370.4	924.9

The above variation is because of different versions or each time freesurfer yields different values? Could you please educate me more on this. Because if the freesurfer version is the issue then I need to run all analysis in one system which will take a lot of time.

Thanks & regards

Vittal