Sorry, it did fall thru the cr cks. Can you try running it with
--no-adjust? When you give it a sign (ie, --pos), it assumes that the
input values and threshold are -log10(p) and then adjusts the threshold
for a single-tailed (signed) test, which means that it subtracts
log10(2) = 0.3 from the threshold. So it's really using 0.5-0.3=0.2 as
the threshold. Hope that made sense ...
doug
Emily Cooper wrote:
hi,
sorry to bother the mailinglist again, but i haven't received a
response to this question. i just wanted to make sure that it hadn't
slipped through the cracks. any help would be very much appreciated,
emily
On 6/1/07, Emily Cooper <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
hi,
i am having a strange problem with mri_surfcluster.
i give it the following command line:
mri_surfcluster --in
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh
--subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos
--minarea 6 --sum
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt
and i get this result in the summary:
# Cluster Growing Summary (mri_surfcluster )
# $Id: mri_surfcluster.c,v 1.26.2.4 <http://1.26.2.4> 2006/07/13
17:50:28 greve Exp $
# $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
# CreationTime 2007/06/01-19:04:15-GMT
# cmdline mri_surfcluster --in
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh
--subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos
--minarea 6 --sum
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt
# cwd /disks/gpfs/fmri/emily.permutations/correlation.permutations
# sysname Linux
# hostname andrew.bsd.uchicago.edu <http://andrew.bsd.uchicago.edu>
# machine i686
# FixVertexAreaFlag = 1
#
# Input
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh
# Frame Number 0
# srcsubj fsaverage
# hemi lh
# surface white
# SUBJECTS_DIR /home/ecooper/subjects
# Minimum Threshold 0.5
# Maximum Threshold 1
# Threshold Sign pos
# AdjustThreshWhenOneTail 1
# Area Threshold 6 mm^2
# Overall max 0.632052 at vertex 5494
# Overall min 0.12689 at vertex 750
# NClusters 2
# Total Cortical Surface Area 70394.7 (mm^2)
# FixMNI = 1
#
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs
1 0.632 5494 85426.29 -50.2 -16.0 -7.2 161181
2 0.223 9300 23.61 -31.7 -26.7 9.9 68
the problem is that this is just entirely incorrect. when i view
the input dataset in tksurfer, it's clear just from scanning over
the vertices that 161181 out of 163842 total of them do not have
intensity values between .5 and 1 (thmin and thmx), let alone in a
giant cluster together. furthermore, when i make a historgram of a
text file containing these intensity values, it shows that the
majority of them are less than .5, and thus shouldn't be
recognized as part of a cluster based on my specifications in the
mri_surfcluster command:
$breaks
[1] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35
0.40 0.45
[13] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
$counts
[1] 10 205 1320 3881 7834 12333 16777 20168 21369 20405
17219 13789
[13] 10453 7479 4897 2988 1599 737 283 81 14 1
$intensities
[1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547
[6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211
[11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233
[16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746
[21] 0.0017089635 0.0001220688
$density
[1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547
[6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211
[11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233
[16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746
[21] 0.0017089635 0.0001220688
$mids
[1] -0.075 -0.025 0.025 0.075 0.125 0.175 0.225 0.275
0.325 0.375
[11] 0.425 0.475 0.525 0.575 0.625 0.675 0.725 0.775
0.825 0.875
[21] 0.925 0.975
any ideas as to what is going wrong here? am i using the thmin and
thmax flags wrong?
thanks so much,
emily
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Douglas N. Greve, Ph.D.
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[EMAIL PROTECTED]
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