Hello,

I found a possible bug in mri_surfcluster, but it may be linked specifically to average7 and no other srcsubjects (but I haven't checked that).  When I run mri_surfcluster with cluster simulation data, the size is reported at a seemingly arbitrary number, based on the fact that the #of vertices does not change.  And the mgh output in null (a blank surface is displayed). 

However when I run mri_surfcluster with cluster simulation data,  but  specify srcsubject, it works correctly.  This seems like a bug, because I think when surfcluster runs csd files it reads the srcsubject from the csd files, and no other srcsubject should be compatible with the data, therefore it must know the srcsubject in both usages, but in one case it works and the other it doesn't. 

Thanks,
Rob


surflcluster with threshold of 1.3
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ    NVtxs
   1       -2.217  145639    413.11     -6.4   38.4    5.0   418
   2       -1.836   29811    141.08    -11.9   53.2   19.0   178
   3       -1.532   16680    111.99    -11.1   19.1   22.6   178
   4       -1.400   83520     17.42     -3.2   11.4   17.5    23

surfcluster using csd files
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ    CWP    CWPLow    CWPHi   NVtxs
   1       -2.217  145639    275.40     -6.4   38.4    5.0  0.01190  0.01050  0.01330   418
   2       -1.836   29811     94.06    -11.9   53.2   19.0  0.50970  0.50330  0.51610   178
   3       -1.532   16680     74.66    -11.1   19.1   22.6  0.64580  0.63970  0.65190   178
   4       -1.400   83520     11.61     -3.2   11.4   17.5  0.97920  0.97740  0.98100    23


Apparently this is the right way to do it:
with csd files, but specify srcsubj average7:

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ    CWP    CWPLow    CWPHi   NVtxs
   1       -2.217  145639    413.11     -6.4   38.4    5.0  0.00010  0.00000  0.00020   418
   2       -1.836   29811    141.08    -11.9   53.2   19.0  0.27000  0.26430  0.27570   178
   3       -1.532   16680    111.99    -11.1   19.1   22.6  0.40500  0.39870  0.41130   178
   4       -1.400   83520     17.42     -3.2   11.4   17.5  0.96970  0.96750  0.97190    23

------- freesurfer-Linux-centos4_x86_64-dev-20070802 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/dev
FSFAST_HOME       /usr/local/freesurfer/dev/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR      /space/ventzl/1/users/SUBJECTS_DIR
MNI_DIR           /usr/local/freesurfer/dev/mni
FSL_DIR           /usr/local/freesurfer/dev/fsl

# PWD:  /space/ventzl/1/users/SUBJECTS_DIR

mri_surfcluster \
--src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \
--csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \
--sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \
--ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \

# overlay shows no clusters (tried at 0.5 as well in case it is a binary map)
tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh

mri_surfcluster \
--really-use-average7 \
--src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \
--csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \
--csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \
--sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \
--ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \
--srcsubj average7

# overlay does show the clusters
tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh

 
-- 

Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2611
Charlestown, MA 02129
email: levy@nmr.mgh.harvard.edu
phone: 617-726-1908
fax: 617-726-4078

http://nmr.mgh.harvard.edu/manoachlab