thanks so much! that seems to have done the trick,
emily
On 6/4/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
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) = 0.3from 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 ecooper@uchicago.edu 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 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 # 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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