Hi Freesurfer experts,

Qdec does not appear to allow me to automatically extract mean values for significant clusters for each participant, so I have been doing this using command line after running the original analysis in Qdec. However, I have found that there are some differences in the significant clusters between the two. The command line I am using is:

mri_glmfit-sim --glmdir TRSCtrl_Vocab_DODS --cache 2 abs --cwp 0.01

I believe that this should correspond to analysis in Qdec using the preset threshold of 2 and Monte-Carlo Null-Z Simulation value of 2.0 (0.01).

The significant clusters from Qdec are:

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ    CWP    CWPLow    CWPHi   NVtxs   Annot

   1        7.740  109023    669.23     -6.1  -12.5   47.0  0.00120  0.00080  0.00170  1618  paracentral

   2        5.854   63055   1542.69    -19.0  -73.2   -3.6  0.00010  0.00000  0.00020  1913  lingual

   3        5.393  127437   1063.38    -23.4   -6.9  -28.0  0.00010  0.00000  0.00020  2069  entorhinal

   4        5.026  112833    788.05    -13.9  -45.3   38.9  0.00010  0.00000  0.00020  1660  precuneus

   5        4.726  141529    523.23    -34.4   -5.7   10.9  0.00760  0.00650  0.00870  1456  insula

   6        4.413   23898    863.24    -13.4   25.1   26.4  0.00010  0.00000  0.00020  1495  superiorfrontal

   7        3.819   21492    874.38    -17.8  -72.7   29.0  0.00010  0.00000  0.00020  1321  precuneus


Whereas from the command line:

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs   Annot

   1        7.740  109023    668.36     56.9  -11.3   35.0  0.00050  0.00020  0.00080  1618  postcentral

   2        5.854   63055   1328.30     52.2  -58.3   -8.8  0.00010  0.00000  0.00020  1913  inferiortemporal

   3        5.393  127437   1004.26     32.5   -2.8  -38.4  0.00010  0.00000  0.00020  1950  fusiform

   4        5.026  112833    782.44     54.3  -41.2   42.3  0.00010  0.00000  0.00020  1660  supramarginal

   5        4.413   23898    780.09     56.5    2.1    6.1  0.00010  0.00000  0.00020  1495  precentral

   6        3.819   21492    673.28     46.3  -59.1   31.8  0.00050  0.00020  0.00080  1321  inferiorparietal


When I view the glmfit clusters in free view they do appear very similar to the ones in Qdec, but there is one less significant clusters and obviously the cluster names are different. Am I using the correct command line to extract this information? 

Many thanks,

Cassie