Re: [Freesurfer] No clusters found after Monte Carlo simulation

can you send the command, terminal output, and log file?

On 09/24/2013 06:04 PM, ye tian wrote:

Dear Doug, Thank you! I tried 500 iterations (I am aware that people usually do

...

10,000), but the program threw a "memory corruption" error. I have

freesurfer 5.3. My ram is 4.0GB and the virtual memory is 7.8GB. Would you please shine some light on what's going on? I can't seem to find an executable solution from the archive. Thank you very much! Sincerely, Ye

On Tue, Sep 24, 2013 at 3:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

You need much more than 5 iterations! If you are doing whole
hemisphere
analysis, then you can use the precomputed tables.

doug


On 09/24/2013 01:46 PM, ye tian wrote:
> Dear Freesurfers,
> Sorry for having posted an incorrect question. I basically ran
> *mri_glmfit-sim *on both hemispheres and tried both *--sim-sign neg
> *and *--sim-sign pos*. Although I only had 5 iterations, I found no
> significant clusters on any case. Does that mean that I accept the
> null hypothesis?
> PS: I found in
>
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23324.html
> that 10,000 iterations are commonly used.
> Thank you very much!
>
>
> On Mon, Sep 23, 2013 at 9:47 PM, ye tian <tianye730@gmail.com
<mailto:tianye730@gmail.com>
> <mailto:tianye730@gmail.com <mailto:tianye730@gmail.com>>> wrote:
>
>     Dear Freesurfers,
>     I used the following command line to find significant clusters
>     after glm analysis (before MC clusters attached)
>     mri_glmfit-sim \
>       --glmdir lh.meditation_age.glmdir \
>       --sim mc-z 5 4 mc-z.negative \
>       --sim-sign neg --cwpvalthresh 0.05\
>       --overwrite
>     I didn't find any, i.e., there are no clusters listed in file
>     mc-z.negative.sig.cluster.summary. Does this mean that I should
>     accept the null hypothesis for the whole cortex?
>     Also, how many iterations of mc do people typically perform? I
>     guess it doesn't make a difference if I do 1000 iterations
instead
>     of 5 anyways.
>     Thank you very much!
>     Sincerely,
>     Ye
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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