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Hello Mathew, I was reporting the console output and not the Lmax file. The Lmax file looks great; I am now seeing the correct numbers of local maxima. Thanks a lot for your help! Best regards Alex On Tue, Jul 27, 2010 at 10:35 AM, Matthew Webster <[log in to unmask]>wrote: > Hello, > Interesting, this looks like output that should be written to the > console, rather than the Lmax file - can you confirm the two are identical? > > Many Regards > > Matthew > > Thanks a lot, Mathew. > > Here is part of the Lmax output that I get in response to the cluster > command: cluster -i N18_Kurth_dAI_g7_zfrm_avg.nii.gz -t .2 --mm -n 5 > --connectivity=26 --olmax=Lmax > > Cluster Index Voxels Z-MAX Z-MAX X (mm) Z-MAX Y (mm) Z-MAX Z > (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z (mm) > 25 7471 2.19 36 20 0 41.6 22 8.69 > 24 4496 0.877 -32 18 4 -37.4 21.9 7.18 > 23 2754 0.524 6 12 46 4.32 13.7 43.5 > 22 2102 0.5 64 -28 30 59.1 -31.7 35.4 > 21 1374 0.439 -62 -32 26 -61.1 -31.9 30.7 > ...... > > Best > Alex > > On Mon, Jul 26, 2010 at 10:58 AM, Matthew Webster <[log in to unmask] > > wrote: > >> Hi, >> I am seeing the correct numbers of local Maxima reported in the Lmax >> file ( 5 entries for the bigger clusters ): >> >> Cluster Index Z x y z >> 25 2.19 36 20 0 >> 25 0.546 52 10 0 >> 25 0.504 36 46 30 >> 25 0.344 44 50 16 >> 25 0.331 42 4 34 >> 24 0.877 -32 18 4 >> 24 0.503 -36 40 30 >> 24 0.32 -28 40 -12 >> 24 0.293 -38 -8 -12 >> 24 0.282 -52 8 10 >> <edit> >> >> can you paste in the contents of your Lmax file so we can check for >> discrepancies? >> >> Many Regards >> >> Matthew >> >> >> Hi Mathew, >> >> I am sorry i meant -t .20 and not -t 2. Could you change the threshold and >> see what i am doing wrong here? >> >> Thank you >> >> Alex >> >> On Mon, Jul 26, 2010 at 10:03 AM, Matthew Webster < >> [log in to unmask]> wrote: >> >>> Hello, >>> Thank you for the upload - it looks like your image only has a >>> single cluster, comprised of 4 voxels, after thresholding - In this case >>> cluster is only able to report one local maximum. >>> >>> Many Regards >>> >>> Matthew >>> >>> >>> Hi Matthew >>> >>> Thanks for your response. >>> >>> The six reference number for this upload session is 860510 . >>> >>> Best >>> >>> Alex >>> >>> On Mon, Jul 26, 2010 at 5:29 AM, Matthew Webster < >>> [log in to unmask]> wrote: >>> >>>> Hi, >>>> Can you upload your input image to: >>>> >>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >>>> >>>> and let me know the 6-digit reference number? >>>> >>>> Many Regards >>>> >>>> Matthew >>>> >>>> >>>> Dear Fslers, >>>> >>>> I am trying to use the cluster command to find peak coordinates within >>>> large clusters of functional connectivity maps. >>>> >>>> The command that I am using is this: >>>> cluster -i SWT_zfrm.avg.nii.gz -t 2 --mm -n 5 --connectivity=26 >>>> --olmax=Lmax >>>> >>>> Instead of outputting 5 local maxima for each cluster, it only gives 1 >>>> as if the argument -n is being ignored. >>>> >>>> Could you tell me what am I going wrong? >>>> >>>> Thank you >>>> >>>> Best >>>> Alex >>>> >>>> >>>> >>> >>> >> >> > >