Where is this data located? I cant find it under /space/ventzl/1/users/SUBJECTS_DIR
Robert Levy wrote:
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
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