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: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
