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