thanks so much! that seems to have done the trick, emily
On 6/4/07, Doug Greve <[EMAIL PROTECTED]> 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 <[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 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 > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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