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